This notebook generates the following figures for the manuscript:

Required inputs to run notebook:

R functions:

  • maf_functions.R ## Input SNV file:
  • SNV_info_allcaller.csv
  • SNV_info_with_transcriptionerror_binom.csv ## Metadata outlining samples within the matrix
  • Edited_metadata.csv
# Load necessary packages
library('ggplot2')
library('plyr')
library('tidyverse')
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
## ✓ tibble  3.1.1     ✓ dplyr   1.0.7
## ✓ tidyr   1.1.3     ✓ stringr 1.4.0
## ✓ readr   2.0.1     ✓ forcats 0.5.1
## ✓ purrr   0.3.4
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::arrange()   masks plyr::arrange()
## x purrr::compact()   masks plyr::compact()
## x dplyr::count()     masks plyr::count()
## x dplyr::failwith()  masks plyr::failwith()
## x dplyr::filter()    masks stats::filter()
## x dplyr::id()        masks plyr::id()
## x dplyr::lag()       masks stats::lag()
## x dplyr::mutate()    masks plyr::mutate()
## x dplyr::rename()    masks plyr::rename()
## x dplyr::summarise() masks plyr::summarise()
## x dplyr::summarize() masks plyr::summarize()
library('dplyr')
library('glue')
library('vcfR')
## 
##    *****       ***   vcfR   ***       *****
##    This is vcfR 1.12.0 
##      browseVignettes('vcfR') # Documentation
##      citation('vcfR') # Citation
##    *****       *****      *****       *****
library('tools')
library('seqinr')
## 
## Attaching package: 'seqinr'
## The following object is masked from 'package:vcfR':
## 
##     write.fasta
## The following object is masked from 'package:dplyr':
## 
##     count
## The following object is masked from 'package:plyr':
## 
##     count
library('plotly')
## 
## Attaching package: 'plotly'
## The following objects are masked from 'package:plyr':
## 
##     arrange, mutate, rename, summarise
## The following object is masked from 'package:ggplot2':
## 
##     last_plot
## The following object is masked from 'package:stats':
## 
##     filter
## The following object is masked from 'package:graphics':
## 
##     layout

Set working directory

workdirectory= "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols/" # set this as its own variable so it is super easy to change later
knitr::opts_knit$set(root.dir = workdirectory)  # this should set the rmd root directory so you don't have to type out 'workdirectory' later on (you still can if you want it doesn't matter)
getwd()  # this should tell you what directory you are working in
## [1] "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols"

#load vivaldi scripts (process all the vcf files and output a single dataframe)

source(glue('{workdirectory}scripts/maf_functions/read_reference_fasta_dna.R')) 
source(glue('{workdirectory}scripts/maf_functions/arrange_gt_data.R'))
source(glue('{workdirectory}scripts/maf_functions/arrange_no_gt_data.R'))
source(glue('{workdirectory}scripts/maf_functions/arrange_gt_varscan.R'))
source(glue('{workdirectory}scripts/maf_functions/add_metadata.R'))
source(glue('{workdirectory}scripts/maf_functions/filter_variants.R'))
source(glue('{workdirectory}scripts/maf_functions/prepare_annotations.R'))
source(glue('{workdirectory}scripts/maf_functions/snpeff_info.R'))
source(glue('{workdirectory}scripts/maf_functions/shannon_entropy.R'))
source(glue('{workdirectory}scripts/maf_functions/plot_shannon.R'))
source(glue('{workdirectory}scripts/maf_functions/tally_it.R'))
source(glue('{workdirectory}scripts/maf_functions/tstv_ratio.R'))
source(glue('{workdirectory}scripts/maf_functions/tstv_plot.R'))
source(glue('{workdirectory}scripts/maf_functions/snv_location.R'))

Run arrange_gt_data on ivar, timo, haplotypecaller, mutect2, freebayes data under standard setting

vcf_df = arrange_gt_data( glue('{workdirectory}/analysis_final/'), glue('{workdirectory}/analysis_final/Reference_coding.fa'), annotated = 'no', ntlist=c('A','G','T','C'))
## Number of chroms in fasta: 3
## Length of input files: 485
## Input vcf files include: c("/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_ivar_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_hc_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_freebayes_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_timo_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_undetermined.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_undetermined.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_undetermined.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_undetermined.fas_BWA_mutect2_standard_unfiltered.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_undetermined.fas_BWA_timo_standard.vcf")
## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 208
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 208
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 208
##   row_num: 0
## 
Processed variant: 208
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 581
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 581
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 581
##   row_num: 0
## 
Processed variant: 581
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 166
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 166
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 166
##   row_num: 0
## 
Processed variant: 166
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 363
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 363
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 363
##   row_num: 0
## 
Processed variant: 363
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 47
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 158
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 158
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 158
##   row_num: 0
## 
Processed variant: 158
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 575
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 575
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 575
##   row_num: 0
## 
Processed variant: 575
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 144
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 144
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 144
##   row_num: 0
## 
Processed variant: 144
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 370
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 370
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 370
##   row_num: 0
## 
Processed variant: 370
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 46
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 0
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## No variant data: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_freebayes_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 0
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## No variant data: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_hc_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 0
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## No variant data: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_ivar_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 0
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## No variant data: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_mutect2_standard_unfiltered
## Sample name is: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 0
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## No variant data: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_timo_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 4
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 4
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 4
##   row_num: 0
## 
Processed variant: 4
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## No snps for sample: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_freebayes_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 10
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 10
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 10
##   row_num: 0
## 
Processed variant: 10
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 0
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## No variant data: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_ivar_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 12
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 12
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 12
##   row_num: 0
## 
Processed variant: 12
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 0
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## No variant data: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_timo_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 45
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 47
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 45
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 41
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 41
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 41
##   row_num: 0
## 
Processed variant: 41
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 45
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 0
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## No variant data: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_freebayes_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 0
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## No variant data: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_hc_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 0
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## No variant data: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_ivar_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 1
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 1
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 1
##   row_num: 0
## 
Processed variant: 1
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 1
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 1
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 1
##   row_num: 0
## 
Processed variant: 1
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 4
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 4
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 4
##   row_num: 0
## 
Processed variant: 4
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 3
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 3
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 3
##   row_num: 0
## 
Processed variant: 3
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 0
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## No variant data: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_ivar_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 5
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 5
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 5
##   row_num: 0
## 
Processed variant: 5
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 2
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 2
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 2
##   row_num: 0
## 
Processed variant: 2
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 0
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## No variant data: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_freebayes_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 0
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## No variant data: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_hc_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 0
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## No variant data: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_ivar_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 0
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## No variant data: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_mutect2_standard_unfiltered
## Sample name is: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 0
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## No variant data: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_timo_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 51
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 51
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 51
##   row_num: 0
## 
Processed variant: 51
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 79
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 79
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 79
##   row_num: 0
## 
Processed variant: 79
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 50
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 100
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 100
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 100
##   row_num: 0
## 
Processed variant: 100
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 35
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 35
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 35
##   row_num: 0
## 
Processed variant: 35
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 45
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 72
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 72
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 72
##   row_num: 0
## 
Processed variant: 72
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 46
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 75
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 75
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 75
##   row_num: 0
## 
Processed variant: 75
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 46
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 46
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 83
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 83
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 83
##   row_num: 0
## 
Processed variant: 83
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 48
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 126
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 126
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 126
##   row_num: 0
## 
Processed variant: 126
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 46
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 45
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 63
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 63
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 63
##   row_num: 0
## 
Processed variant: 63
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 47
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 110
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 110
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 110
##   row_num: 0
## 
Processed variant: 110
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 37
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 37
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 37
##   row_num: 0
## 
Processed variant: 37
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 47
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 75
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 75
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 75
##   row_num: 0
## 
Processed variant: 75
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 48
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 68
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 68
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 68
##   row_num: 0
## 
Processed variant: 68
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 46
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 43
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 82
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 82
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 82
##   row_num: 0
## 
Processed variant: 82
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 44
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 91
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 91
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 91
##   row_num: 0
## 
Processed variant: 91
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 17
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 17
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 17
##   row_num: 0
## 
Processed variant: 17
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 42
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 42
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 42
##   row_num: 0
## 
Processed variant: 42
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 82
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 82
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 82
##   row_num: 0
## 
Processed variant: 82
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 45
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 90
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 90
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 90
##   row_num: 0
## 
Processed variant: 90
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 43
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 38
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 38
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 38
##   row_num: 0
## 
Processed variant: 38
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 76
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 76
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 76
##   row_num: 0
## 
Processed variant: 76
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 38
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 38
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 38
##   row_num: 0
## 
Processed variant: 38
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 73
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 73
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 73
##   row_num: 0
## 
Processed variant: 73
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 11
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 11
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 11
##   row_num: 0
## 
Processed variant: 11
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 43
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 73
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 73
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 73
##   row_num: 0
## 
Processed variant: 73
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 45
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 89
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 89
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 89
##   row_num: 0
## 
Processed variant: 89
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 43
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 50
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 58
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 58
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 58
##   row_num: 0
## 
Processed variant: 58
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 50
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 76
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 76
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 76
##   row_num: 0
## 
Processed variant: 76
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 40
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 40
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 40
##   row_num: 0
## 
Processed variant: 40
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 43
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 117
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 117
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 117
##   row_num: 0
## 
Processed variant: 117
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 45
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 144
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 144
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 144
##   row_num: 0
## 
Processed variant: 144
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 41
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 41
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 41
##   row_num: 0
## 
Processed variant: 41
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 47
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 67
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 67
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 67
##   row_num: 0
## 
Processed variant: 67
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 49
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 74
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 74
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 74
##   row_num: 0
## 
Processed variant: 74
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 45
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 39
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 39
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 39
##   row_num: 0
## 
Processed variant: 39
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 79
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 79
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 79
##   row_num: 0
## 
Processed variant: 79
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 44
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 116
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 116
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 116
##   row_num: 0
## 
Processed variant: 116
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 18
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 18
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 18
##   row_num: 0
## 
Processed variant: 18
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 47
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 64
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 64
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 64
##   row_num: 0
## 
Processed variant: 64
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 48
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 93
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 93
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 93
##   row_num: 0
## 
Processed variant: 93
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 42
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 42
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 42
##   row_num: 0
## 
Processed variant: 42
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 33
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 33
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 33
##   row_num: 0
## 
Processed variant: 33
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 78
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 78
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 78
##   row_num: 0
## 
Processed variant: 78
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 33
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 33
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 33
##   row_num: 0
## 
Processed variant: 33
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 104
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 104
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 104
##   row_num: 0
## 
Processed variant: 104
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 12
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 12
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 12
##   row_num: 0
## 
Processed variant: 12
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 41
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 41
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 41
##   row_num: 0
## 
Processed variant: 41
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 73
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 73
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 73
##   row_num: 0
## 
Processed variant: 73
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 45
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 94
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 94
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 94
##   row_num: 0
## 
Processed variant: 94
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 52
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 52
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 52
##   row_num: 0
## 
Processed variant: 52
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 75
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 75
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 75
##   row_num: 0
## 
Processed variant: 75
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 51
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 51
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 51
##   row_num: 0
## 
Processed variant: 51
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 66
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 66
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 66
##   row_num: 0
## 
Processed variant: 66
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 37
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 37
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 37
##   row_num: 0
## 
Processed variant: 37
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 42
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 42
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 42
##   row_num: 0
## 
Processed variant: 42
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 61
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 61
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 61
##   row_num: 0
## 
Processed variant: 61
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 45
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 83
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 83
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 83
##   row_num: 0
## 
Processed variant: 83
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 50
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 73
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 73
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 73
##   row_num: 0
## 
Processed variant: 73
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 50
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 101
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 101
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 101
##   row_num: 0
## 
Processed variant: 101
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 45
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 46
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 70
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 70
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 70
##   row_num: 0
## 
Processed variant: 70
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 47
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 64
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 64
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 64
##   row_num: 0
## 
Processed variant: 64
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 41
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 41
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 41
##   row_num: 0
## 
Processed variant: 41
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 46
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 75
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 75
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 75
##   row_num: 0
## 
Processed variant: 75
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 48
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 100
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 100
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 100
##   row_num: 0
## 
Processed variant: 100
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 45
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 38
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 38
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 38
##   row_num: 0
## 
Processed variant: 38
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 73
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 73
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 73
##   row_num: 0
## 
Processed variant: 73
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 42
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 42
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 42
##   row_num: 0
## 
Processed variant: 42
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 72
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 72
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 72
##   row_num: 0
## 
Processed variant: 72
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 20
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 20
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 20
##   row_num: 0
## 
Processed variant: 20
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 43
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 68
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 68
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 68
##   row_num: 0
## 
Processed variant: 68
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 45
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 76
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 76
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 76
##   row_num: 0
## 
Processed variant: 76
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 29
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 29
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 29
##   row_num: 0
## 
Processed variant: 29
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 66
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 66
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 66
##   row_num: 0
## 
Processed variant: 66
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 30
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 30
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 30
##   row_num: 0
## 
Processed variant: 30
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 79
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 79
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 79
##   row_num: 0
## 
Processed variant: 79
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 11
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 11
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 11
##   row_num: 0
## 
Processed variant: 11
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 45
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 69
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 69
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 69
##   row_num: 0
## 
Processed variant: 69
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 45
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 98
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 98
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 98
##   row_num: 0
## 
Processed variant: 98
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 45
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 48
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 62
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 62
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 62
##   row_num: 0
## 
Processed variant: 62
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 48
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 62
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 62
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 62
##   row_num: 0
## 
Processed variant: 62
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 37
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 37
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 37
##   row_num: 0
## 
Processed variant: 37
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 46
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 82
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 82
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 82
##   row_num: 0
## 
Processed variant: 82
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 47
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 69
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 69
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 69
##   row_num: 0
## 
Processed variant: 69
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 40
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 40
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 40
##   row_num: 0
## 
Processed variant: 40
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 48
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 73
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 73
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 73
##   row_num: 0
## 
Processed variant: 73
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 50
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 85
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 85
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 85
##   row_num: 0
## 
Processed variant: 85
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 40
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 40
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 40
##   row_num: 0
## 
Processed variant: 40
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 64
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 64
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 64
##   row_num: 0
## 
Processed variant: 64
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 43
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 85
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 85
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 85
##   row_num: 0
## 
Processed variant: 85
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 23
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 23
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 23
##   row_num: 0
## 
Processed variant: 23
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 46
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 69
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 69
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 69
##   row_num: 0
## 
Processed variant: 69
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 47
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 112
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 112
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 112
##   row_num: 0
## 
Processed variant: 112
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 30
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 30
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 30
##   row_num: 0
## 
Processed variant: 30
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 69
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 69
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 69
##   row_num: 0
## 
Processed variant: 69
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 28
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 28
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 28
##   row_num: 0
## 
Processed variant: 28
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 62
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 62
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 62
##   row_num: 0
## 
Processed variant: 62
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 11
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 11
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 11
##   row_num: 0
## 
Processed variant: 11
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 45
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 74
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 74
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 74
##   row_num: 0
## 
Processed variant: 74
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 46
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 79
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 79
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 79
##   row_num: 0
## 
Processed variant: 79
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 49
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 66
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 66
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 66
##   row_num: 0
## 
Processed variant: 66
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 50
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 74
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 74
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 74
##   row_num: 0
## 
Processed variant: 74
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 37
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 37
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 37
##   row_num: 0
## 
Processed variant: 37
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 45
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 92
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 92
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 92
##   row_num: 0
## 
Processed variant: 92
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 45
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 129
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 129
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 129
##   row_num: 0
## 
Processed variant: 129
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 43
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 49
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 61
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 61
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 61
##   row_num: 0
## 
Processed variant: 61
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 50
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 77
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 77
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 77
##   row_num: 0
## 
Processed variant: 77
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 44
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 81
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 81
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 81
##   row_num: 0
## 
Processed variant: 81
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 47
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 127
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 127
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 127
##   row_num: 0
## 
Processed variant: 127
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 42
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 42
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 42
##   row_num: 0
## 
Processed variant: 42
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 43
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 78
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 78
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 78
##   row_num: 0
## 
Processed variant: 78
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 47
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 84
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 84
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 84
##   row_num: 0
## 
Processed variant: 84
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 45
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 75
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 75
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 75
##   row_num: 0
## 
Processed variant: 75
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 45
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 90
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 90
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 90
##   row_num: 0
## 
Processed variant: 90
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 19
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 19
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 19
##   row_num: 0
## 
Processed variant: 19
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 46
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 69
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 69
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 69
##   row_num: 0
## 
Processed variant: 69
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 48
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 73
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 73
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 73
##   row_num: 0
## 
Processed variant: 73
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 43
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 36
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 36
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 36
##   row_num: 0
## 
Processed variant: 36
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 132
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 132
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 132
##   row_num: 0
## 
Processed variant: 132
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 37
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 37
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 37
##   row_num: 0
## 
Processed variant: 37
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 103
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 103
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 103
##   row_num: 0
## 
Processed variant: 103
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 12
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 12
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 12
##   row_num: 0
## 
Processed variant: 12
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 43
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 81
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 81
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 81
##   row_num: 0
## 
Processed variant: 81
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 47
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 104
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 104
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 104
##   row_num: 0
## 
Processed variant: 104
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 42
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 42
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 42
##   row_num: 0
## 
Processed variant: 42
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 49
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 80
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 80
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 80
##   row_num: 0
## 
Processed variant: 80
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 52
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 52
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 52
##   row_num: 0
## 
Processed variant: 52
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 84
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 84
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 84
##   row_num: 0
## 
Processed variant: 84
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 40
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 40
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 40
##   row_num: 0
## 
Processed variant: 40
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 46
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 94
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 94
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 94
##   row_num: 0
## 
Processed variant: 94
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 47
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 107
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 107
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 107
##   row_num: 0
## 
Processed variant: 107
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 36
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 36
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 36
##   row_num: 0
## 
Processed variant: 36
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 50
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 95
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 95
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 95
##   row_num: 0
## 
Processed variant: 95
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 53
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 53
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 53
##   row_num: 0
## 
Processed variant: 53
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 68
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 68
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 68
##   row_num: 0
## 
Processed variant: 68
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 45
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 42
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 42
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 42
##   row_num: 0
## 
Processed variant: 42
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 63
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 63
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 63
##   row_num: 0
## 
Processed variant: 63
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 44
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 66
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 66
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 66
##   row_num: 0
## 
Processed variant: 66
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 16
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 16
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 16
##   row_num: 0
## 
Processed variant: 16
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 51
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 51
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 51
##   row_num: 0
## 
Processed variant: 51
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 108
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 108
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 108
##   row_num: 0
## 
Processed variant: 108
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 51
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 51
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 51
##   row_num: 0
## 
Processed variant: 51
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 78
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 78
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 78
##   row_num: 0
## 
Processed variant: 78
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 35
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 35
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 35
##   row_num: 0
## 
Processed variant: 35
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 91
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 91
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 91
##   row_num: 0
## 
Processed variant: 91
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 38
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 38
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 38
##   row_num: 0
## 
Processed variant: 38
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 81
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 81
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 81
##   row_num: 0
## 
Processed variant: 81
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 12
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 12
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 12
##   row_num: 0
## 
Processed variant: 12
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 49
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 139
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 139
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 139
##   row_num: 0
## 
Processed variant: 139
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 52
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 52
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 52
##   row_num: 0
## 
Processed variant: 52
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 137
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 137
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 137
##   row_num: 0
## 
Processed variant: 137
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 46
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 50
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 95
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 95
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 95
##   row_num: 0
## 
Processed variant: 95
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 52
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 52
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 52
##   row_num: 0
## 
Processed variant: 52
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 114
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 114
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 114
##   row_num: 0
## 
Processed variant: 114
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 39
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 39
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 39
##   row_num: 0
## 
Processed variant: 39
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 48
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 70
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 70
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 70
##   row_num: 0
## 
Processed variant: 70
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 48
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 64
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 64
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 64
##   row_num: 0
## 
Processed variant: 64
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 45
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 49
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 127
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 127
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 127
##   row_num: 0
## 
Processed variant: 127
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 50
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 157
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 157
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 157
##   row_num: 0
## 
Processed variant: 157
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 45
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 50
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 71
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 71
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 71
##   row_num: 0
## 
Processed variant: 71
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 50
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 88
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 88
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 88
##   row_num: 0
## 
Processed variant: 88
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 42
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 42
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 42
##   row_num: 0
## 
Processed variant: 42
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 46
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 120
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 120
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 120
##   row_num: 0
## 
Processed variant: 120
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 49
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 139
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 139
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 139
##   row_num: 0
## 
Processed variant: 139
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 44
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 68
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 68
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 68
##   row_num: 0
## 
Processed variant: 68
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 43
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 77
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 77
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 77
##   row_num: 0
## 
Processed variant: 77
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 16
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 16
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 16
##   row_num: 0
## 
Processed variant: 16
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 50
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 164
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 164
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 164
##   row_num: 0
## 
Processed variant: 164
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 51
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 51
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 51
##   row_num: 0
## 
Processed variant: 51
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 156
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 156
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 156
##   row_num: 0
## 
Processed variant: 156
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 45
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 31
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 31
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 31
##   row_num: 0
## 
Processed variant: 31
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 92
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 92
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 92
##   row_num: 0
## 
Processed variant: 92
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 33
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 33
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 33
##   row_num: 0
## 
Processed variant: 33
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 61
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 61
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 61
##   row_num: 0
## 
Processed variant: 61
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 11
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 11
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 11
##   row_num: 0
## 
Processed variant: 11
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 46
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 74
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 74
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 74
##   row_num: 0
## 
Processed variant: 74
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 46
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 115
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 115
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 115
##   row_num: 0
## 
Processed variant: 115
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 43
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 76
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 76
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 76
##   row_num: 0
## 
Processed variant: 76
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 80
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 80
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 80
##   row_num: 0
## 
Processed variant: 80
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 53
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 53
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 53
##   row_num: 0
## 
Processed variant: 53
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 73
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 73
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 73
##   row_num: 0
## 
Processed variant: 73
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 43
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 45
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 77
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 77
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 77
##   row_num: 0
## 
Processed variant: 77
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 48
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 103
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 103
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 103
##   row_num: 0
## 
Processed variant: 103
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 39
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 39
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 39
##   row_num: 0
## 
Processed variant: 39
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 51
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 51
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 51
##   row_num: 0
## 
Processed variant: 51
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 117
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 117
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 117
##   row_num: 0
## 
Processed variant: 117
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 54
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 54
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 54
##   row_num: 0
## 
Processed variant: 54
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 89
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 89
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 89
##   row_num: 0
## 
Processed variant: 89
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 43
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 42
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 42
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 42
##   row_num: 0
## 
Processed variant: 42
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 72
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 72
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 72
##   row_num: 0
## 
Processed variant: 72
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 45
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 98
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 98
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 98
##   row_num: 0
## 
Processed variant: 98
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 19
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 19
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 19
##   row_num: 0
## 
Processed variant: 19
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 47
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 95
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 95
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 95
##   row_num: 0
## 
Processed variant: 95
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 49
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 128
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 128
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 128
##   row_num: 0
## 
Processed variant: 128
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 40
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 40
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 40
##   row_num: 0
## 
Processed variant: 40
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 141
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 141
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 141
##   row_num: 0
## 
Processed variant: 141
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 41
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 41
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 41
##   row_num: 0
## 
Processed variant: 41
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 162
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 162
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 162
##   row_num: 0
## 
Processed variant: 162
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 16
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 16
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 16
##   row_num: 0
## 
Processed variant: 16
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 50
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 126
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 126
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 126
##   row_num: 0
## 
Processed variant: 126
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 50
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 98
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 98
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 98
##   row_num: 0
## 
Processed variant: 98
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 51
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 51
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 51
##   row_num: 0
## 
Processed variant: 51
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 91
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 91
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 91
##   row_num: 0
## 
Processed variant: 91
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 53
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 53
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 53
##   row_num: 0
## 
Processed variant: 53
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 94
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 94
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 94
##   row_num: 0
## 
Processed variant: 94
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 40
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 40
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 40
##   row_num: 0
## 
Processed variant: 40
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 49
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 85
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 85
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 85
##   row_num: 0
## 
Processed variant: 85
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 49
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 102
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 102
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 102
##   row_num: 0
## 
Processed variant: 102
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 50
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 99
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 99
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 99
##   row_num: 0
## 
Processed variant: 99
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 53
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 53
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 53
##   row_num: 0
## 
Processed variant: 53
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 86
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 86
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 86
##   row_num: 0
## 
Processed variant: 86
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 50
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 105
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 105
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 105
##   row_num: 0
## 
Processed variant: 105
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 51
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 51
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 51
##   row_num: 0
## 
Processed variant: 51
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 89
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 89
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 89
##   row_num: 0
## 
Processed variant: 89
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 39
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 39
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 39
##   row_num: 0
## 
Processed variant: 39
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 46
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 88
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 88
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 88
##   row_num: 0
## 
Processed variant: 88
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 49
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 71
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 71
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 71
##   row_num: 0
## 
Processed variant: 71
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 43
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 45
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 77
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 77
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 77
##   row_num: 0
## 
Processed variant: 77
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 47
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 65
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 65
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 65
##   row_num: 0
## 
Processed variant: 65
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 17
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 17
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 17
##   row_num: 0
## 
Processed variant: 17
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 50
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 127
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 127
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 127
##   row_num: 0
## 
Processed variant: 127
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 51
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 51
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 51
##   row_num: 0
## 
Processed variant: 51
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 130
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 130
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 130
##   row_num: 0
## 
Processed variant: 130
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 30
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 30
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 30
##   row_num: 0
## 
Processed variant: 30
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 93
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 93
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 93
##   row_num: 0
## 
Processed variant: 93
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 31
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 31
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 31
##   row_num: 0
## 
Processed variant: 31
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 69
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 69
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 69
##   row_num: 0
## 
Processed variant: 69
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 11
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 11
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 11
##   row_num: 0
## 
Processed variant: 11
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 43
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 85
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 85
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 85
##   row_num: 0
## 
Processed variant: 85
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 46
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 107
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 107
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 107
##   row_num: 0
## 
Processed variant: 107
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 48
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 49
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 32
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 32
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 32
##   row_num: 0
## 
Processed variant: 32
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 43
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 25
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 25
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 25
##   row_num: 0
## 
Processed variant: 25
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 46
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 103
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 103
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 103
##   row_num: 0
## 
Processed variant: 103
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 46
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 110
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 110
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 110
##   row_num: 0
## 
Processed variant: 110
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 42
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 42
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 42
##   row_num: 0
## 
Processed variant: 42
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 22
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 22
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 22
##   row_num: 0
## 
Processed variant: 22
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 30
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 30
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 30
##   row_num: 0
## 
Processed variant: 30
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 22
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 22
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 22
##   row_num: 0
## 
Processed variant: 22
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 25
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 25
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 25
##   row_num: 0
## 
Processed variant: 25
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 19
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 19
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 19
##   row_num: 0
## 
Processed variant: 19
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 39
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 39
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 39
##   row_num: 0
## 
Processed variant: 39
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 97
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 97
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 97
##   row_num: 0
## 
Processed variant: 97
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 42
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 42
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 42
##   row_num: 0
## 
Processed variant: 42
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 80
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 80
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 80
##   row_num: 0
## 
Processed variant: 80
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 20
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 20
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 20
##   row_num: 0
## 
Processed variant: 20
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 1
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 1
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 1
##   row_num: 0
## 
Processed variant: 1
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## No snps for sample: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_freebayes_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 7
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 7
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 7
##   row_num: 0
## 
Processed variant: 7
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 1
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 1
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 1
##   row_num: 0
## 
Processed variant: 1
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 8
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 8
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 8
##   row_num: 0
## 
Processed variant: 8
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 3
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 3
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 3
##   row_num: 0
## 
Processed variant: 3
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 35
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 35
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 35
##   row_num: 0
## 
Processed variant: 35
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 105
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 105
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 105
##   row_num: 0
## 
Processed variant: 105
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 38
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 38
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 38
##   row_num: 0
## 
Processed variant: 38
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 126
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 126
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 126
##   row_num: 0
## 
Processed variant: 126
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 17
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 17
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 17
##   row_num: 0
## 
Processed variant: 17
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 15
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 15
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 15
##   row_num: 0
## 
Processed variant: 15
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 22
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 22
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 22
##   row_num: 0
## 
Processed variant: 22
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 15
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 15
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 15
##   row_num: 0
## 
Processed variant: 15
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 31
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 31
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 31
##   row_num: 0
## 
Processed variant: 31
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 14
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 14
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 14
##   row_num: 0
## 
Processed variant: 14
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 50
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 68
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 68
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 68
##   row_num: 0
## 
Processed variant: 68
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 51
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 51
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 51
##   row_num: 0
## 
Processed variant: 51
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 74
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 74
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 74
##   row_num: 0
## 
Processed variant: 74
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 38
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 38
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 38
##   row_num: 0
## 
Processed variant: 38
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 3
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 3
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 3
##   row_num: 0
## 
Processed variant: 3
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 17
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 17
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 17
##   row_num: 0
## 
Processed variant: 17
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 0
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## No variant data: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_ivar_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 24
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 24
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 24
##   row_num: 0
## 
Processed variant: 24
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 4
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 4
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 4
##   row_num: 0
## 
Processed variant: 4
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 49
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 74
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 74
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 74
##   row_num: 0
## 
Processed variant: 74
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 48
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 89
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 89
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 89
##   row_num: 0
## 
Processed variant: 89
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 45
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 28
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 28
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 28
##   row_num: 0
## 
Processed variant: 28
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 27
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 27
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 27
##   row_num: 0
## 
Processed variant: 27
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 20
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 20
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 20
##   row_num: 0
## 
Processed variant: 20
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 72
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 72
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 72
##   row_num: 0
## 
Processed variant: 72
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 22
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 22
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 22
##   row_num: 0
## 
Processed variant: 22
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 45
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 74
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 74
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 74
##   row_num: 0
## 
Processed variant: 74
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 47
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 122
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 122
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 122
##   row_num: 0
## 
Processed variant: 122
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 43
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 43
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 43
##   row_num: 0
## 
Processed variant: 43
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 6
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 6
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 6
##   row_num: 0
## 
Processed variant: 6
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 33
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 33
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 33
##   row_num: 0
## 
Processed variant: 33
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 4
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 4
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 4
##   row_num: 0
## 
Processed variant: 4
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 20
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 20
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 20
##   row_num: 0
## 
Processed variant: 20
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 1
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 1
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 1
##   row_num: 0
## 
Processed variant: 1
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 47
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 70
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 70
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 70
##   row_num: 0
## 
Processed variant: 70
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 47
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 81
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 81
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 81
##   row_num: 0
## 
Processed variant: 81
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 44
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 52
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 52
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 52
##   row_num: 0
## 
Processed variant: 52
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 76
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 76
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 76
##   row_num: 0
## 
Processed variant: 76
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 54
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 54
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 54
##   row_num: 0
## 
Processed variant: 54
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 59
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 59
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 59
##   row_num: 0
## 
Processed variant: 59
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 46
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_freebayes_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 63
##   header_line: 64
##   variant count: 47
##   column count: 10
## 
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element GL
## Extracting gt element DP
## Extracting gt element AD
## Extracting gt element RO
## Extracting gt element QR
## Extracting gt element AO
## Extracting gt element QA
## Extracting gt element MIN_DP
## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_hc_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 30
##   header_line: 31
##   variant count: 72
##   column count: 10
## 
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 72
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 72
##   row_num: 0
## 
Processed variant: 72
## All variants processed
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PL
## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_ivar_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 7
##   header_line: 8
##   variant count: 49
##   column count: 10
## 
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ
## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_mutect2_standard_unfiltered
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 45
##   header_line: 46
##   variant count: 74
##   column count: 10
## 
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 74
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 74
##   row_num: 0
## 
Processed variant: 74
## All variants processed
## Extracting gt element AD
## Extracting gt element AF
## Extracting gt element DP
## Extracting gt element F1R2
## Extracting gt element F2R1
## Extracting gt element GQ
## Extracting gt element GT
## Extracting gt element PGT
## Extracting gt element PID
## Extracting gt element PL
## Extracting gt element PS
## Extracting gt element SB
## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_timo_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 8
##   header_line: 9
##   variant count: 41
##   column count: 10
## 
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 41
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 41
##   row_num: 0
## 
Processed variant: 41
## All variants processed
## Extracting gt element GT
## Extracting gt element AD
## Extracting gt element DP
## Extracting gt element GQ

Run loferq data under standard setting

vcf_df_lofreq = arrange_no_gt_data( glue('{workdirectory}/lofreq/'), glue('{workdirectory}/lofreq/Reference_coding.fa'), annotated = 'no', ntlist=c('A','G','T','C'))
## Number of chroms in fasta: 3
## Length of input files: 97
## Input vcf files include: c("/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_lofreq_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_undetermined.fas_BWA_lofreq_standard.vcf")
## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 496
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 496
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 496
##   row_num: 0
## 
Processed variant: 496
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 511
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 511
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 511
##   row_num: 0
## 
Processed variant: 511
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 0
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## No variant data: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_lofreq_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 4
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 4
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 4
##   row_num: 0
## 
Processed variant: 4
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 48
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 0
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## No variant data: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_lofreq_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 3
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 3
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 3
##   row_num: 0
## 
Processed variant: 3
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 0
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## No variant data: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_lofreq_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 89
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 89
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 89
##   row_num: 0
## 
Processed variant: 89
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 79
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 79
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 79
##   row_num: 0
## 
Processed variant: 79
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 97
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 97
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 97
##   row_num: 0
## 
Processed variant: 97
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 65
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 65
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 65
##   row_num: 0
## 
Processed variant: 65
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 71
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 71
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 71
##   row_num: 0
## 
Processed variant: 71
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 90
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 90
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 90
##   row_num: 0
## 
Processed variant: 90
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 91
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 91
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 91
##   row_num: 0
## 
Processed variant: 91
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 62
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 62
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 62
##   row_num: 0
## 
Processed variant: 62
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 88
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 88
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 88
##   row_num: 0
## 
Processed variant: 88
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 68
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 68
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 68
##   row_num: 0
## 
Processed variant: 68
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 152
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 152
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 152
##   row_num: 0
## 
Processed variant: 152
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 63
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 63
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 63
##   row_num: 0
## 
Processed variant: 63
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 73
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 73
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 73
##   row_num: 0
## 
Processed variant: 73
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 67
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 67
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 67
##   row_num: 0
## 
Processed variant: 67
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 58
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 58
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 58
##   row_num: 0
## 
Processed variant: 58
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 73
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 73
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 73
##   row_num: 0
## 
Processed variant: 73
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 59
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 59
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 59
##   row_num: 0
## 
Processed variant: 59
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 56
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 56
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 56
##   row_num: 0
## 
Processed variant: 56
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 62
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 62
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 62
##   row_num: 0
## 
Processed variant: 62
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 60
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 60
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 60
##   row_num: 0
## 
Processed variant: 60
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 68
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 68
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 68
##   row_num: 0
## 
Processed variant: 68
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 69
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 69
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 69
##   row_num: 0
## 
Processed variant: 69
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 80
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 80
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 80
##   row_num: 0
## 
Processed variant: 80
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 68
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 68
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 68
##   row_num: 0
## 
Processed variant: 68
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 64
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 64
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 64
##   row_num: 0
## 
Processed variant: 64
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 55
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 55
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 55
##   row_num: 0
## 
Processed variant: 55
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 69
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 69
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 69
##   row_num: 0
## 
Processed variant: 69
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 78
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 78
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 78
##   row_num: 0
## 
Processed variant: 78
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 65
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 65
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 65
##   row_num: 0
## 
Processed variant: 65
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 66
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 66
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 66
##   row_num: 0
## 
Processed variant: 66
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 50
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 78
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 78
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 78
##   row_num: 0
## 
Processed variant: 78
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 63
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 63
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 63
##   row_num: 0
## 
Processed variant: 63
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 108
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 108
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 108
##   row_num: 0
## 
Processed variant: 108
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 66
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 66
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 66
##   row_num: 0
## 
Processed variant: 66
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 86
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 86
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 86
##   row_num: 0
## 
Processed variant: 86
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 49
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 49
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 49
##   row_num: 0
## 
Processed variant: 49
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 71
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 71
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 71
##   row_num: 0
## 
Processed variant: 71
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 50
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 134
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 134
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 134
##   row_num: 0
## 
Processed variant: 134
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 72
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 72
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 72
##   row_num: 0
## 
Processed variant: 72
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 66
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 66
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 66
##   row_num: 0
## 
Processed variant: 66
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 82
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 82
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 82
##   row_num: 0
## 
Processed variant: 82
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 91
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 91
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 91
##   row_num: 0
## 
Processed variant: 91
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 56
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 56
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 56
##   row_num: 0
## 
Processed variant: 56
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 89
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 89
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 89
##   row_num: 0
## 
Processed variant: 89
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 78
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 78
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 78
##   row_num: 0
## 
Processed variant: 78
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 138
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 138
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 138
##   row_num: 0
## 
Processed variant: 138
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 116
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 116
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 116
##   row_num: 0
## 
Processed variant: 116
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 64
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 64
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 64
##   row_num: 0
## 
Processed variant: 64
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 190
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 190
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 190
##   row_num: 0
## 
Processed variant: 190
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 64
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 64
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 64
##   row_num: 0
## 
Processed variant: 64
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 126
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 126
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 126
##   row_num: 0
## 
Processed variant: 126
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 64
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 64
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 64
##   row_num: 0
## 
Processed variant: 64
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 194
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 194
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 194
##   row_num: 0
## 
Processed variant: 194
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 63
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 63
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 63
##   row_num: 0
## 
Processed variant: 63
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 88
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 88
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 88
##   row_num: 0
## 
Processed variant: 88
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 57
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 57
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 57
##   row_num: 0
## 
Processed variant: 57
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 80
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 80
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 80
##   row_num: 0
## 
Processed variant: 80
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 116
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 116
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 116
##   row_num: 0
## 
Processed variant: 116
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 64
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 64
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 64
##   row_num: 0
## 
Processed variant: 64
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 83
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 83
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 83
##   row_num: 0
## 
Processed variant: 83
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 194
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 194
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 194
##   row_num: 0
## 
Processed variant: 194
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 139
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 139
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 139
##   row_num: 0
## 
Processed variant: 139
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 101
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 101
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 101
##   row_num: 0
## 
Processed variant: 101
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 67
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 67
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 67
##   row_num: 0
## 
Processed variant: 67
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 83
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 83
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 83
##   row_num: 0
## 
Processed variant: 83
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 94
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 94
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 94
##   row_num: 0
## 
Processed variant: 94
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 82
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 82
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 82
##   row_num: 0
## 
Processed variant: 82
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 67
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 67
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 67
##   row_num: 0
## 
Processed variant: 67
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 121
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 121
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 121
##   row_num: 0
## 
Processed variant: 121
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 72
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 72
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 72
##   row_num: 0
## 
Processed variant: 72
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 98
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 98
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 98
##   row_num: 0
## 
Processed variant: 98
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 39
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 39
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 39
##   row_num: 0
## 
Processed variant: 39
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 105
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 105
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 105
##   row_num: 0
## 
Processed variant: 105
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 35
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 35
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 35
##   row_num: 0
## 
Processed variant: 35
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 87
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 87
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 87
##   row_num: 0
## 
Processed variant: 87
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 9
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 9
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 9
##   row_num: 0
## 
Processed variant: 9
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 108
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 108
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 108
##   row_num: 0
## 
Processed variant: 108
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 33
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 33
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 33
##   row_num: 0
## 
Processed variant: 33
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 81
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 81
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 81
##   row_num: 0
## 
Processed variant: 81
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 12
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 12
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 12
##   row_num: 0
## 
Processed variant: 12
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 82
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 82
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 82
##   row_num: 0
## 
Processed variant: 82
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 37
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 37
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 37
##   row_num: 0
## 
Processed variant: 37
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 75
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 75
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 75
##   row_num: 0
## 
Processed variant: 75
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 6
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 6
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 6
##   row_num: 0
## 
Processed variant: 6
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 67
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 67
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 67
##   row_num: 0
## 
Processed variant: 67
## All variants processed
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 55
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 55
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 55
##   row_num: 0
## 
Processed variant: 55
## All variants processed
## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_lofreq_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 17
##   header_line: 18
##   variant count: 73
##   column count: 8
## 
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 73
##   Character matrix gt cols: 8
##   skip: 0
##   nrows: 73
##   row_num: 0
## 
Processed variant: 73
## All variants processed
#Modify lofreq df for later rbind 
vcf_df_lofreq = vcf_df_lofreq  %>% add_column(REF_COUNT = NA) %>% add_column(ALT_COUNT = NA) %>% add_column(ChromKey = NA)
vcf_df_lofreq$AF = NULL

Run varscan data under standard setting

vcf_df_var = arrange_gt_data_varscan( glue('{workdirectory}/varscan/'), glue('{workdirectory}/varscan/Reference_coding.fa'), annotated = 'no', ntlist=c('A','G','T','C'))
## Number of chroms in fasta: 3
## Length of input files: 94
## Input vcf files include: c("/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_varscan_standard.vcf", 
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_undetermined.fas_BWA_varscan_standard.vcf")
## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 140
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 140
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 140
##   row_num: 0
## 
Processed variant: 140
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 118
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 118
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 118
##   row_num: 0
## 
Processed variant: 118
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 0
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## No variant data: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_varscan_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 38
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 38
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 38
##   row_num: 0
## 
Processed variant: 38
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 0
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## No variant data: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_varscan_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 47
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 44
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 36
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 36
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 36
##   row_num: 0
## 
Processed variant: 36
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 44
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 30
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 30
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 30
##   row_num: 0
## 
Processed variant: 30
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 44
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 39
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 39
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 39
##   row_num: 0
## 
Processed variant: 39
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 29
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 29
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 29
##   row_num: 0
## 
Processed variant: 29
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 44
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 47
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 38
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 38
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 38
##   row_num: 0
## 
Processed variant: 38
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 24
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 24
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 24
##   row_num: 0
## 
Processed variant: 24
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 44
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 37
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 37
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 37
##   row_num: 0
## 
Processed variant: 37
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 44
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 24
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 24
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 24
##   row_num: 0
## 
Processed variant: 24
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 41
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 41
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 41
##   row_num: 0
## 
Processed variant: 41
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 30
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 30
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 30
##   row_num: 0
## 
Processed variant: 30
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 47
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 48
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 37
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 37
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 37
##   row_num: 0
## 
Processed variant: 37
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 47
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 28
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 28
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 28
##   row_num: 0
## 
Processed variant: 28
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 47
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 47
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 37
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 37
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 37
##   row_num: 0
## 
Processed variant: 37
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 50
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 50
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 50
##   row_num: 0
## 
Processed variant: 50
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 26
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 26
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 26
##   row_num: 0
## 
Processed variant: 26
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 44
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 47
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 42
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 42
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 42
##   row_num: 0
## 
Processed variant: 42
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 44
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 34
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 34
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 34
##   row_num: 0
## 
Processed variant: 34
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 47
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 47
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 48
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 48
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 44
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 38
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 38
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 38
##   row_num: 0
## 
Processed variant: 38
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 47
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 26
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 26
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 26
##   row_num: 0
## 
Processed variant: 26
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 44
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 44
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 44
##   row_num: 0
## 
Processed variant: 44
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 30
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 30
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 30
##   row_num: 0
## 
Processed variant: 30
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 19
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 19
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 19
##   row_num: 0
## 
Processed variant: 19
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 38
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 38
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 38
##   row_num: 0
## 
Processed variant: 38
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 1
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 1
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 1
##   row_num: 0
## 
Processed variant: 1
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 32
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 32
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 32
##   row_num: 0
## 
Processed variant: 32
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 15
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 15
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 15
##   row_num: 0
## 
Processed variant: 15
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 47
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 0
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 0
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 0
##   row_num: 0
## 
Processed variant: 0
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## No variant data: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_varscan_standard
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 47
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 47
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 47
##   row_num: 0
## 
Processed variant: 47
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 15
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 15
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 15
##   row_num: 0
## 
Processed variant: 15
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 2
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 2
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 2
##   row_num: 0
## 
Processed variant: 2
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 45
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 45
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 45
##   row_num: 0
## 
Processed variant: 45
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 46
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 46
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 46
##   row_num: 0
## 
Processed variant: 46
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_varscan_standard
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 23
##   header_line: 24
##   variant count: 48
##   column count: 10
## 
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 48
##   Character matrix gt cols: 10
##   skip: 0
##   nrows: 48
##   row_num: 0
## 
Processed variant: 48
## All variants processed
## Extracting gt element GT
## Extracting gt element GQ
## Extracting gt element SDP
## Extracting gt element DP
## Extracting gt element RD
## Extracting gt element AD
## Extracting gt element FREQ
## Extracting gt element PVAL
## Extracting gt element RBQ
## Extracting gt element ABQ
## Extracting gt element RDF
## Extracting gt element RDR
## Extracting gt element ADF
## Extracting gt element ADR
vcf_df_var = vcf_df_var %>% add_column(ChromKey = NA)

#Merge df for all the callers

vcf_df = rbind(vcf_df, vcf_df_lofreq, vcf_df_var)

Modify vcf_df for the later merging of vcf_df and the metadata

vcf_df$sample_name = vcf_df$sample
#print(head(vcf_df))
vcf_df = vcf_df %>% separate(sample_name, c("filename", "vcf_inputs"), sep='[.]')

read in metadata

metadata = read.csv("Edited_metadata.csv", header = T)
#print(head(metadata))

Merge the metadata with vcf_df

vcf_full = merge(vcf_df, metadata, by=c('filename'), all.x = T) 
#print(head(vcf_full))

#checking to make sure that the dimensions after merging are identical

dim(vcf_df)
## [1] 37707    21
dim(vcf_full)
## [1] 37707    41
#Dimensions are off by 10, checking the names of the files that are in the metadata but NOT included in our variant data
not_included = setdiff(levels(factor(vcf_full$filename)), levels(factor(vcf_df$filename)))
print(not_included)
## character(0)
#Check manually the metadata to confirm that we do not have variants in the above samples because they are WT and/or water controls 

#Print off the names so they should all be wt control or empty
levels(factor((vcf_full %>% filter(filename %in% not_included))$SampleInfo))
## character(0)
#Re-merge to remove these files and check with Mohammed that 0 variants were found in these samples and weren't missed during analysis 
vcf_full = merge(vcf_df, metadata, by=c('filename'), all.x = TRUE)  # this will keep ALL variant data

#rechecking the dim - they should be identical now 
dim(vcf_df)
## [1] 37707    21
dim(vcf_full)
## [1] 37707    41

#Modify vcf to remove files that are not used

message ("I'm removing samples that we are uncertain because of the metadata")
## I'm removing samples that we are uncertain because of the metadata
vcf_full = vcf_full %>% filter(Use == "yes") %>% unique() 

Merge vcf_full with SNV_info to select TP, FP, TN

SNVinfo = read.csv("SNV_info_allcaller.csv", header = T, check.names = FALSE)

#Right now the NA segment is treated as NA values in the df, so need to fix that
SNVinfo$CHROM = as.character(SNVinfo$CHROM)
SNVinfo$CHROM[is.na(SNVinfo$CHROM)] <- "NA"

#Right now the SNV_info is in wide format, change that into long format using pivot_longer
# we need the columns Copy_number and Expected_freq to be able to merge with your variant data, after merging na will appear in 'True' variables if it is a false-positive call! 
SNVinfo = SNVinfo %>% pivot_longer(c("10000000", "1000000","100000","10000","1000"), names_to = "TrueExpectedCopyNumber", values_to = "Copy_number")

SNVinfo = SNVinfo %>% pivot_longer(c("0.5", "0.25", "0.125",    '0.0625',   '0.0313',   '0.0156',   '0.0078',   '0.0039'), names_to = "TrueExpectedFrequency", values_to = "Expected_freq")

# Change the name of variant caller info
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_ivar_standard", "ivar")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_timo_standard", "timo")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_hc_standard", "hc")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_mutect2_standard_unfiltered", "mutect2")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_freebayes_standard", "freebayes")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_lofreq_standard", "lofreq")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_varscan_standard", "varscan")


#Merge SNVinfo with vcf_full
vcf_plus = merge(vcf_full, SNVinfo, by=c("POS","CHROM", "REF", "ALT", "Copy_number", "Expected_freq", "vcf_inputs"), all = TRUE)

#Replace NAs with 0
# use = 0 instead of = "0" so the following if_else can work (numeric values to use >, =, <)
vcf_plus$Expected_freq[is.na(vcf_plus$Expected_freq)] = 0
vcf_plus$ALT_FREQ[is.na(vcf_plus$ALT_FREQ)] = 0

vcf_plus$TrueExpectedCopyNumber[is.na(vcf_plus$TrueExpectedCopyNumber)] = 0
vcf_plus$TrueExpectedFrequency[is.na(vcf_plus$TrueExpectedFrequency)] = 0

#Using if.else to determine TP, FP, FN
vcf_plus = vcf_plus %>% mutate(type = ifelse( ALT_FREQ > 0 & TrueExpectedFrequency == 0, "FP",
                                   ifelse(ALT_FREQ == 0 & TrueExpectedFrequency > 0, "FN",
                                   ifelse(ALT_FREQ > 0 & TrueExpectedFrequency > 0, "TP", "NA"))))
message("Remove 10^7 samples due to technical issues")
## Remove 10^7 samples due to technical issues
vcf_plus = vcf_plus %>% filter(Copy_number != "10^7")

What is the relationship between observed and expected allele frequency estimates? Fig 3C & Fig S6A

# Use only TPs - so we can answer the question: of the TP snps that we did find, how close were they to the expected freq?
TP = vcf_plus %>% filter (type == "TP", Rep == "rep1")

# Set colors for callers
tool_colors = c('#CC2F42', # freebayes - red
                 '#35B6E9', # hc - bright blue
                 '#009E73', # ivar - green
                 '#F9BECD', # lofreq - pink
                 '#F0E442', # mutect2 - yellow
                 '#CCD2EB', # timo - light purple
                 '#9B9E9A') # varscan, grey
tools = c("freebayes", "hc", "ivar", "lofreq", "mutect2", "timo", "varscan")
names(tool_colors) = tools
tool_colScale_fill <- scale_fill_manual(name = "Variant Caller",values = tool_colors)
tool_colScale <- scale_colour_manual(name = "Variant Caller",values = tool_colors)

TPmedian = TP %>% group_by(TrueExpectedFrequency, CHROM) %>% summarise(medianfreq = median(ALT_FREQ))
## `summarise()` has grouped output by 'TrueExpectedFrequency'. You can override using the `.groups` argument.
TP = merge(TP, TPmedian, by = c("TrueExpectedFrequency", "CHROM"))


# X-axis: True expected freq (FP should have an expected freq of 0)
# Order the grid so it would be PB2, HA, NA
TP$CHROM = factor(TP$CHROM, levels=c('PB2', 'HA', 'NA'))

Fig3A = ggplot(TP %>% filter(!FerretID %in% c("Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix44")), aes(x = factor(round(medianfreq, digits = 3)), y = ALT_FREQ, color = vcf_inputs))+
  labs(x="Median observed Frequency", y= "Observed Frequency") +
  geom_point(width = 0.2, alpha = 0.3, position=position_dodge(width = 0.5)) + 
  tool_colScale+
  facet_grid(.~CHROM, scales = "free", space = "free")  + 
  theme_bw() +
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 13))+ 
  theme(legend.key = element_blank(),
                strip.background = element_rect(colour="black", fill="white"),
                axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
  stat_summary(fun = "median", geom = "point", col = "black",size = 2,shape = 18,fill = "red")
## Warning: Ignoring unknown parameters: width
print(Fig3A)

ggsave(Fig3A,
       filename = glue("{workdirectory}/figures_new/Fig3A.png"),
       width = 15,
       height = 5, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(Fig3A,
       filename = glue("{workdirectory}/figures_pdf_new/Fig3A.pdf"),
       width = 15,
       height = 5, limitsize=FALSE)#, useDingbats = FALSE)

# Set colors for copy numbers
cn_colors <- c( '#BBBBBB', '#999999', 
                '#777777', 
                '#555555', 
                '#333333')

copy_numbers = c("10^2", "10^3", "10^4", "10^5", "10^6")
names(cn_colors) = copy_numbers
cn_colScale_fill <- scale_fill_manual(name = "Copy Number",values = cn_colors)
cn_colScale <- scale_colour_manual(name = "Copy Number",values = cn_colors)

FigS6A = ggplot(TP, aes(x = as.numeric(Expected_freq), y = ALT_FREQ, color = Copy_number))+
  labs(x="Expected Frequency", y= "Observed Frequency") +
  geom_point(alpha = 0.8) + 
  facet_grid(CHROM~vcf_inputs)  + 
  theme_bw() +
  cn_colScale+
  geom_abline(slope=1)+
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 13))+ 
  theme(legend.key = element_blank(),
                strip.background = element_rect(colour="black", fill="white"),
                axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS6A)

ggsave(FigS6A,
       filename = glue("{workdirectory}/figures_new/FigS6A.png"),
       width = 16,
       height = 6.5, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(FigS6A,
       filename = glue("{workdirectory}/figures_pdf_new/FigS6A.pdf"),
       width = 16,
       height = 6.5, limitsize=FALSE)#, useDingbats = FALSE)

Coverage plots - Fig S5C & S5D

# make a coverage plot for all samples across genome position
flu_covinfo = read.csv("cov_data.tsv", sep = "", header = T)
flu_covinfo = flu_covinfo %>% filter (name != "000000000-K4LKV_l01_undetermined.fas_BWA") 
flu_covinfo$segment[is.na(flu_covinfo$segment)] <- "NA"

flu_cov = separate(flu_covinfo,name,sep = "_", 
                   into = c("IDK", "IDKk", "IDkkk", "Sample", "Rep")) %>% 
  select(!c("IDK","IDKk","IDkkk"))
## Warning: Expected 5 pieces. Additional pieces discarded in 495972 rows [1, 2, 3,
## 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
flu_cov$Rep<-gsub(".fas","",as.character(flu_cov$Rep))
flu_cov = flu_cov %>% filter(Sample != "Control01") %>% filter(Sample != "Control02")%>% filter(Sample != "Control04")%>% filter(Sample != "Control05")

# Set gradient colors for all samples
sample_colors = c("#373737", "#323232", "#2D2D2D","#282828", "#232323","#1E1E1E", "#191919", "#141414", "#0F0F0F", "#0A0A0A","#3C3C3C","#414141", "#464646", "#4B4B4B", "#505050", "#555555", "#5A5A5A", "#5F5F5F", "#646464", "#696969","#6E6E6E","#737373", "#787878", "#7D7D7D",  "#828282", "#878787","#8C8C8C", "#919191", "#969696", "#9B9B9B",  "#ADADAD","#A5A5A5", "#AAAAAA", "#AFAFAF", "#B4B4B4", "#B9B9B9", "#BEBEBE", "#C3C3C3","#C8C8C8",  "#CDCDCD", "#D2D2D2", "#D7D7D7", "#DCDCDC", "#E1E1E1")
samples = c("Mix01", "Mix02", "Mix03", "Mix04", "Mix05", "Mix06", "Mix07", "Mix08", "Mix09", "Mix10", "Mix11","Mix12", "Mix13", "Mix14", "Mix15", "Mix16", "Mix17", "Mix18", "Mix19", "Mix20", "Mix21", "Mix22", "Mix23", "Mix24", "Mix25", "Mix26", "Mix27", "Mix28", "Mix29", "Mix30", "Mix31", "Mix32", "Mix33", "Mix34", "Mix35", "Mix36", "Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix43", "Mix44")
names(sample_colors) = samples
sample_colScale_fill <- scale_fill_manual(name = "Samples",values = sample_colors)
sample_colScale <- scale_colour_manual(name = "Samples",values = sample_colors)

flu_cov$segment = factor(flu_cov$segment, levels=c("PB2", "HA", "NA"))
FigS5C = ggplot(data = flu_cov, aes(x=ntpos, y=log10(totalcount), color = Sample)) +
        geom_line(aes(group=Sample), size = 1) +
        theme_bw() +
  sample_colScale+
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 15))+ 
        theme(legend.key = element_blank(),
              strip.background = element_rect(colour="black", fill="white"),
              axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)) +
        facet_grid(Rep~segment, scales = "free_x") +
        xlab("Nucleotide Position") +
        ylab("Log10 Read Depth")
print(FigS5C)

ggsave(FigS5C,
       filename = glue("{workdirectory}/FigS5C.png"),
       width = 12,
       height = 7, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(FigS5C,
       filename = glue("{workdirectory}/figures_pdf/FigS5C.pdf"),
       width = 12,
       height = 7, limitsize=FALSE)#, useDingbats = FALSE)

## what are the bad samples? need to exclude them from the analysis 
bad_samples = flu_cov %>% filter (log10(totalcount) < 2)
unique(bad_samples$Sample)
## [1] "Mix37" "Mix38" "Mix39" "Mix40" "Mix41" "Mix42" "Mix44"
flu_cov = flu_cov %>% filter(!Sample %in% c("Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix44"))

##calculate the average coverage for each sample. then plot: X-axis: sample, y-axis:avg coverage, geom_point

cov_avg = flu_cov %>% group_by(Sample, segment, Rep) %>% summarise(sample_avg_cov = mean(totalcount))
## `summarise()` has grouped output by 'Sample', 'segment'. You can override using the `.groups` argument.
# Set color for replicates
rep12_colors = c('#2F142B', # rep1
                '#43668B')# rep2
rep12names = c("rep1", "rep2")
names(rep12_colors) = rep12names
rep12_colScale_fill <- scale_fill_manual(name = "Rep",values = rep12_colors)
rep12_colScale <- scale_colour_manual(name = "Rep",values = rep12_colors)

FigS5D = ggplot(cov_avg, aes(x = Sample, y = log10(sample_avg_cov), color = Rep))+
  labs(x="Sample", y= "Log10(Average Coverage)") +
  geom_point(alpha = 0.8) + 
  facet_grid(.~segment,scales = "free")  + 
  rep12_colScale+
  theme_bw() +
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 15))+ 
  theme(legend.key = element_blank(),
                strip.background = element_rect(colour="black", fill="white"),
                axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS5D)

ggsave(FigS5D,
       filename = glue("{workdirectory}/FigS5D.png"),
       width = 12,
       height = 5, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(FigS5D,
       filename = glue("{workdirectory}/figures_pdf/FigS5D.pdf"),
       width = 12,
       height = 5, limitsize=FALSE)#, useDingbats = FALSE)

Create the replicate df

# separate rep1 from rep2
rep1 = vcf_plus %>% filter(Rep == "rep1") %>% filter(!FerretID %in% c("Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix44"))
rep2 = vcf_plus %>% filter(Rep == "rep2") %>% filter(!FerretID %in% c("Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix44"))

# merge the replicates 
replicates = merge(rep1, rep2, 
by.x =c('CHROM', "Copy_number", "POS", "Expected_freq", "REF", "ALT", "ChromKey", "vcf_inputs", "Use", "Cohort", "repname"),
by.y = c('CHROM', "Copy_number", "POS", "Expected_freq", "REF", "ALT", "ChromKey", "vcf_inputs", "Use", "Cohort", "Sample"),  all = T)

#Change NA to zero 
replicates$ALT_FREQ.x[is.na(replicates$ALT_FREQ.x)] = 0
replicates$ALT_FREQ.y[is.na(replicates$ALT_FREQ.y)] = 0
replicates$type.x[is.na(replicates$type.x)] = "NONE"
replicates$type.y[is.na(replicates$type.y)] = "NONE"
# Remove the controls for this analysis 
replicates = replicates %>% filter(!Copy_number == "control")

# specify the four categories 

replicates = replicates %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp", 
                               ifelse(type.x == type.y & type.x == 'FP', "both_fp", 
                               ifelse(type.x == "TP" & type.y != "TP", "rep1_tp", 
                               ifelse(type.x != "TP" & type.y == 'TP', 'rep2_tp', 
                               ifelse(type.x == 'FP' & type.y != 'FP' | type.x != 'FP' & type.y == 'FP', 'single_fp', "NA"))))))

How we find the transcription errors - Fig S5E

replicates$VAR = paste0(replicates$CHROM, '_', replicates$POS,'_', replicates$ALT)
#replicates %>% filter(Category == "both_fp")
reduced_reps_df = replicates %>% filter(Category == "both_fp") %>%
    select(CHROM, POS, ALT,ALT_FREQ.y,VAR, ALT_FREQ.x, REF, Category, Expected_freq, Copy_number, vcf_inputs) %>%
      unique()
reduced_reps_df = reduced_reps_df %>% group_by(Expected_freq, CHROM, POS, ALT, VAR,vcf_inputs) %>%
                    add_tally(name = 'copy_number_count') %>%
                    unique() %>% ungroup() %>% group_by(Copy_number, CHROM, POS, ALT, VAR,vcf_inputs) %>%
                  add_tally(name = 'Expected_freq_count') %>% ungroup() %>%
                  group_by(Copy_number, CHROM, POS, ALT, VAR, Expected_freq) %>%
                  add_tally(name = 'vcf_type_count') %>% ungroup()

# Filter for transcription errors 
transcription_err = levels(factor((reduced_reps_df %>% filter(copy_number_count >1 &
                                                                 Expected_freq_count > 1 &
                                                                 vcf_type_count >=2 &
                                                                 vcf_inputs %in% c("varscan","ivar","timo","freebayes"))                                                    %>% unique())$VAR))
transcription_errors = reduced_reps_df %>% filter(VAR %in% transcription_err)
transcription_errors$error_type = "pre_MRTPCR"
other_errors = reduced_reps_df %>% filter(!VAR %in% levels(factor(transcription_errors$VAR)))
other_errors$error_type = "post_MRTPCR"

error_df= rbind(transcription_errors, other_errors)

error_df$CHROM = factor(error_df$CHROM, levels = c("PB2", "HA", "NA"))
error_df$vcf_inputs = factor(error_df$vcf_inputs, levels = c("lofreq","hc","mutect2","freebayes","timo", "ivar","varscan"))

# Set color for nucleotides
nt_colors = c('#d7191c', # red - A
'#abd9e9', # light blue - T
'#fdae61', # orange - C 
'#2c7bb6') # dark blue - G
nt = c("A", "T", "C", "G")
names(nt_colors) = nt
nt_colScale_fill <- scale_fill_manual(name = "Nucleotide",values = nt_colors)
nt_colScale <- scale_colour_manual(name = "Nucleotide",values = nt_colors)

FigS5E = ggplot(error_df, aes(x=VAR, y=vcf_inputs,fill = ALT)) +
    geom_tile(alpha = 0.8) +
    facet_grid(error_type~CHROM, scales = 'free')+
    nt_colScale_fill+
    theme(axis.text.x=element_blank(), #remove x axis labels
          axis.ticks.x=element_blank(),
          legend.key = element_blank(),
                  strip.background = element_rect(colour= "black", fill= "white"))
print(FigS5E)

ggsave(FigS5E,
       filename = glue("{workdirectory}/figures_new/FigS5E.png"),
       width = 10,
       height = 5, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(FigS5E,
       filename = glue("{workdirectory}/figures_pdf_new/FigS5E.pdf"),
       width = 10,
       height = 5, limitsize=FALSE)#, useDingbats = FALSE)

what’s the relationship between allele freq estimates between replicates? - Figure S7A

## Change the category of transcription errors we found into "transcription error"
Transcription_error = replicates %>% filter(CHROM %in% c("PB2", "HA", "NA"), POS %in% c("596", "114", "176", "2102", "2197", "2207", "1367"), ALT %in% c("A" , "G")) %>% filter(Category == "both_fp") %>%  mutate(Category = replace(Category, Category == "both_fp", "pre_MRTPCR"))

replicates = replicates %>% filter (!(CHROM == "HA"& POS == "596"& ALT == "A" & Category == "both_fp")) %>% filter (!(CHROM == "PB2"& POS == "114"& ALT == "A"& Category == "both_fp")) %>% filter (!(CHROM == "PB2"& POS == "176"& ALT == "A"& Category == "both_fp")) %>% filter (!(CHROM == "PB2"& POS == "2102"& ALT == "G"& Category == "both_fp")) %>% filter (!(CHROM == "PB2"& POS == "2197"& ALT == "G"& Category == "both_fp")) %>% filter (!(CHROM == "PB2"& POS == "2207"& ALT == "G"& Category == "both_fp")) %>% filter (!(CHROM == "NA"& POS == "1367"& ALT == "A"& Category == "both_fp")) 

replicates = rbind(replicates, Transcription_error)
                                                 
#Set colors for categories
category_colors = c('#2F142B', # both TP
            '#E86F3F', # both FP
            '#5E2A59', # one rep TP
            '#5E2A59', # one rep TP
            '#F2A07B',# one rep FP 
            "#F0E442")#preMRTPCR 
categories = c('both_tp','both_fp','rep1_tp','rep2_tp','single_fp', 'pre_MRTPCR' )
names(category_colors) = categories
category_colScale_fill <- scale_fill_manual(name = "Category",values = category_colors)
category_colScale <- scale_colour_manual(name = "Category",values = category_colors)

#Plot: observed freq in rep1 against observed freq in rep2
#Create layers so that the both_fp category are on the toppest layer of the graph for better visualization (otherwise it will be blocked by both_tp becuse there are a lot of them)
FPlayer = replicates %>%  filter(Category == "both_fp")
Othertype = replicates %>%  filter(!Category == "both_fp")

## Annotate the percentage of TP & FPs shared between two replicates for each caller 
ivar_both_fp = replicates %>%  filter(Category == "both_fp", vcf_inputs =="ivar")
ivar_both_tp = replicates %>%  filter(Category == "both_tp", vcf_inputs =="ivar")

hc_both_fp = replicates %>%  filter(Category == "both_fp", vcf_inputs =="hc")
hc_both_tp = replicates %>%  filter(Category == "both_tp", vcf_inputs =="hc")

timo_both_fp = replicates %>%  filter(Category == "both_fp", vcf_inputs =="timo")
timo_both_tp = replicates %>%  filter(Category == "both_tp", vcf_inputs =="timo")

mutect2_both_fp = replicates %>%  filter(Category == "both_fp", vcf_inputs =="mutect2")
mutect2_both_tp = replicates %>%  filter(Category == "both_tp", vcf_inputs =="mutect2")

lofreq_both_fp = replicates %>%  filter(Category == "both_fp", vcf_inputs =="lofreq")
lofreq_both_tp = replicates %>%  filter(Category == "both_tp", vcf_inputs =="lofreq")

varscan_both_fp = replicates %>%  filter(Category == "both_fp", vcf_inputs =="varscan")
varscan_both_tp = replicates %>%  filter(Category == "both_tp", vcf_inputs =="varscan")

freebayes_both_fp = replicates %>%  filter(Category == "both_fp", vcf_inputs =="freebayes")
freebayes_both_tp = replicates %>%  filter(Category == "both_tp", vcf_inputs =="freebayes")

## Create an additional data frame to hold the text annotations 
Annotation_fp = data.frame(
  label = c( "0.18%","1.7%","0%","2.7%","10.4%","19.6%","22.3%"), 
  vcf_inputs_f = c( "varscan", "ivar","timo","freebayes", "mutect2", "hc", "lofreq"))


FPlayer$vcf_inputs_f = factor(FPlayer$vcf_inputs, levels=c("varscan", "ivar","timo","freebayes", "mutect2", "hc", "lofreq"))
Othertype$vcf_inputs_f = factor(Othertype$vcf_inputs, levels=c("varscan", "ivar","timo","freebayes", "mutect2", "hc", "lofreq"))

# Zoom in the figure, looking at observed frequency less or equal to 0.25
Othertype_v2 = Othertype %>% filter(ALT_FREQ.x <= 0.25, ALT_FREQ.y <=0.25)
FPlayer_v2 = FPlayer %>% filter(ALT_FREQ.x <= 0.25, ALT_FREQ.y <=0.25)

FigS7A = ggplot() +  
    geom_point(data= Othertype_v2, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
    geom_point(data=FPlayer_v2, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
    labs(x="Observed Frequency Rep1", y= "Observed Frequency Rep2") +
    category_colScale +
    theme_bw() +
    facet_grid(.~vcf_inputs_f) +
    theme(legend.key = element_blank(),
                strip.background = element_rect(colour="black", fill="white"),
                axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
    annotate(geom = "segment", x = 0.1, y = 0.025, xend = 0.025, yend = 0.015, curvature = .3, arrow = arrow(length = unit(1, "mm"))) +
  geom_text(x = 0.13, y = 0.028, aes(label = label), data = Annotation_fp, size = 3)
## Warning: Ignoring unknown parameters: width

## Warning: Ignoring unknown parameters: width
## Warning: Ignoring unknown parameters: curvature
print(FigS7A)

ggsave(FigS7A,
       filename = glue("{workdirectory}/figures_new/FigS7A.png"),
       width = 15,
       height = 3, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(FigS7A,
       filename = glue("{workdirectory}/figures_pdf_new/FigS7A.pdf"),
       width = 15,
       height = 3, limitsize=FALSE)#, useDingbats = FALSE)

SNV map: showing both engineered SNVs and in-vitro transcription errors - FigureS5A

SNVTransErr = read.csv("Transcription_error_binom.csv", header = T, check.names = FALSE)
SNVTransErr$CHROM = as.character(SNVTransErr$CHROM)
SNVTransErr$CHROM[is.na(SNVTransErr$CHROM)] <- "NA"
SNVinfo$CHROM[is.na(SNVinfo$CHROM)] <- "NA"

SNVinfo$CHROM = factor(SNVinfo$CHROM, levels=c('PB2', 'HA', 'NA'))
SNVTransErr$CHROM = factor(SNVTransErr$CHROM, levels=c('PB2', 'HA', 'NA'))

FigS5A =  ggplot() + 
            geom_segment(data = SNVinfo, aes(x = POS, xend = POS, y=0, yend = 1),alpha = 0.8, color = "azure4") + 
            geom_segment(data = SNVTransErr, aes(x = POS, xend = POS, y=0, yend = 1, linetype= "Pre-MRTPCR error"),alpha = 0.8, color = "red") + 
            facet_grid(.~CHROM, scales = "free_x", space = 'free_x') +
            ylab("") + 
            xlab("Genome position") + 
            scale_x_continuous(expand = c(0, 0))+
            theme(panel.background = element_blank(),
                      axis.line = element_line(colour = "gray"),
                      legend.key = element_blank(),
                      strip.background = element_rect(colour="gray", fill="white"),
                      axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
                        panel.border = element_rect(colour='gray', fill = NA),
                         axis.ticks.y = element_blank(),        
            axis.text.y = element_blank(), legend.position="bottom",
                  legend.title=element_blank())
print(FigS5A)

ggsave(FigS5A,
       filename = glue("{workdirectory}/Figures/FigS5A.png"),
       width = 17,
       height = 2, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(FigS5A,
       filename = glue("{workdirectory}/figures_pdf/FigS5A.pdf"),
       width = 17,
       height = 2, limitsize=FALSE)#, useDingbats = FALSE)

# SNV map without transcription error 
SNVmap_noTE =  ggplot() + 
            geom_segment(data = SNVinfo, aes(x = POS, xend = POS, y=0, yend = 1),alpha = 1, color = "azure4", size = 1) + 
            #geom_segment(data = SNVTransErr, aes(x = POS, xend = POS, y=0, yend = 1, linetype= "Pre-MRTPCR error"),alpha = 0.8, color = "red") + 
            facet_grid(.~CHROM, scales = "free_x", space = 'free_x') +
            ylab("") + 
            xlab("Genome position") + 
            scale_x_continuous(expand = c(0, 0))+
            theme(panel.background = element_blank(),
                      axis.line = element_line(colour = "gray"),
                      legend.key = element_blank(),
                      strip.background = element_rect(colour="gray", fill="white"),
                      axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
                        panel.border = element_rect(colour='gray', fill = NA),
                         axis.ticks.y = element_blank(),        
            axis.text.y = element_blank(), legend.position="bottom",
                  legend.title=element_blank())
print(SNVmap_noTE)

ggsave(SNVmap_noTE,
       filename = glue("{workdirectory}/Figures/SNVmap_noTE.png"),
       width = 17,
       height = 2, limitsize=FALSE)#, useDingbats = FALSE)

So right now, create a new SNV_info that include the transcription error positions, the rest of the analysis should be based on this SNV_info

SNVinfo = read.csv("SNV_info_with_transcriptionerror_binom.csv", header = T, check.names = FALSE)

#Right now the NA segment is treated as NA values in the df, so need to fix that
SNVinfo$CHROM = as.character(SNVinfo$CHROM)
SNVinfo$CHROM[is.na(SNVinfo$CHROM)] <- "NA"

#Right now the SNV_info is in wide format, change that into long format using pivot_longer
# we need the columns Copy_number and Expected_freq to be able to merge with your variant data, after merging na will appear in 'True' variables if it is a false-positive call! 
SNVinfo = SNVinfo %>% pivot_longer(c("10000000", "1000000","100000","10000","1000"), names_to = "TrueExpectedCopyNumber", values_to = "Copy_number")

SNVinfo = SNVinfo %>% pivot_longer(c("0.5", "0.25", "0.125",    '0.0625',   '0.0313',   '0.0156',   '0.0078',   '0.0039'), names_to = "TrueExpectedFrequency", values_to = "Expected_freq")

# Change the name of variant caller info
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_ivar_standard", "ivar")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_timo_standard", "timo")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_hc_standard", "hc")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_mutect2_standard_unfiltered", "mutect2")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_freebayes_standard", "freebayes")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_lofreq_standard", "lofreq")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_varscan_standard", "varscan")

#Merge SNVinfo with vcf_full
vcf_plus = merge(vcf_full, SNVinfo, by=c("POS","CHROM", "REF", "ALT", "Copy_number", "Expected_freq", "vcf_inputs", "Rep"), all = TRUE)

#Replace NAs with 0
# use = 0 instead of = "0" so the following if_else can work (numeric values to use >, =, <)
vcf_plus$Expected_freq[is.na(vcf_plus$Expected_freq)] = 0
vcf_plus$ALT_FREQ[is.na(vcf_plus$ALT_FREQ)] = 0

vcf_plus$TrueExpectedCopyNumber[is.na(vcf_plus$TrueExpectedCopyNumber)] = 0

vcf_plus$TrueExpectedFrequency[is.na(vcf_plus$TrueExpectedFrequency)] = 0

#test831 = vcf_plus %>% filter(POS == "831" & CHROM == "HA")

#Using if.else to determine TP, FP, FN
vcf_plus = vcf_plus %>% mutate(type = ifelse( ALT_FREQ > 0 & TrueExpectedFrequency == 0, "FP",
                                   ifelse(ALT_FREQ == 0 & TrueExpectedFrequency > 0, "FN",
                                   ifelse(ALT_FREQ > 0 & TrueExpectedFrequency > 0, "TP", "NA"))))

vcf_plus = vcf_plus %>% filter(Copy_number != "10^7") 

How well the variant callers agreed on the frequency of the variants predicted? - FigureS6B Note: Need to combine all these figures to make the whole S6B

#plot the frequency of a variant in one caller against the frequency in each of the other callers
Timofreq = vcf_plus %>% filter(vcf_inputs == "timo", Rep == "rep1")
hcfreq = vcf_plus %>% filter(vcf_inputs == "hc", Rep == "rep1")
ivarfreq = vcf_plus %>% filter(vcf_inputs == "ivar", Rep == "rep1")
freebayesfreq = vcf_plus %>% filter(vcf_inputs == "freebayes", Rep == "rep1")
varscanfreq = vcf_plus %>% filter(vcf_inputs == "varscan", Rep == "rep1")

# Timo vs Haplotypecaller
timohc = merge(Timofreq, hcfreq, 
         by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
         by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)

timohc = timohc%>%filter(!Copy_number == "control")
timohc$type.x[is.na(timohc$type.x)] <- "NA"
timohc$type.y[is.na(timohc$type.y)] <- "NA"

timohc = timohc %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp", 
                               ifelse(type.x == type.y & type.x == 'FP', "both_fp", 
                               ifelse(type.x == type.y & type.x == 'FN', "both_fn",
                               ifelse(type.x == "TP" & type.y != "TP", "caller1_tp", 
                               ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp', 
                               ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
                               ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
                                      "NA"))))))))

#Set colors
category_colors_1 = c( '#E86F3F', '#2F142B','#5E2A59','#5E2A59', '#F2A07B','#43668B', '#43668B')
categories_1 = c('both_fp','both_tp','caller1_tp','caller2_tp', "single_fp", "single_fn", "both_fn")
names(category_colors_1) = categories_1
category_colScale_fill_1 <- scale_fill_manual(name = "Category",values = category_colors_1)
category_colScale_1 <- scale_colour_manual(name = "Category",values = category_colors_1)

#calculate both TP%
timohc_bothtp = timohc %>% filter(Category == "both_tp")
#calculate both FP%
timohc_counts = timohc %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
timohc_counts$both_tp[is.na(timohc_counts$both_tp)] = 0
#timohc_counts$both_fp[is.na(timohc_counts$both_fp)] = 0
timohc_counts$both_fn[is.na(timohc_counts$both_fn)] = 0
sum(timohc_counts$both_fp)/(sum(timohc_counts$both_fp)+sum(timohc_counts$both_tp))
## Warning: Unknown or uninitialised column: `both_fp`.

## Warning: Unknown or uninitialised column: `both_fp`.
## [1] 0
Figtimohc = ggplot(timohc, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category)) + 
  labs(x="timo", y= "hc") +
  geom_point(width = 0.2, alpha = 0.5) +
   category_colScale_1  +
  theme_bw()+
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 15))+
  annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 61.6%", hjust = "left")+
  annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 0%", hjust = "left")
## Warning: Ignoring unknown parameters: width
  #facet_grid(.~Copy_number)
print(Figtimohc)
## Warning: Removed 1535 rows containing missing values (geom_point).

ggsave(Figtimohc,
       filename = glue("{workdirectory}/figures_new/Figtimohc.png"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 1535 rows containing missing values (geom_point).
ggsave(Figtimohc,
       filename = glue("{workdirectory}/figures_pdf/Figtimohc.pdf"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 1535 rows containing missing values (geom_point).
#timo vs ivar
timoivar = merge(Timofreq, ivarfreq, 
         by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
         by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)

timoivar = timoivar%>%filter(!Copy_number == "control")
timoivar$type.x[is.na(timoivar$type.x)] <- "NA"
timoivar$type.y[is.na(timoivar$type.y)] <- "NA"

timoivar = timoivar %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp", 
                               ifelse(type.x == type.y & type.x == 'FP', "both_fp", 
                               ifelse(type.x == type.y & type.x == 'FN', "both_fn",
                               ifelse(type.x == "TP" & type.y != "TP", "caller1_tp", 
                               ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp', 
                               ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
                               ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
                                      "NA"))))))))

#calculate both TP%
timoivar_bothtp = timoivar %>% filter(Category == "both_tp")
#calculate both FP%
timoivar_counts = timoivar %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
timoivar_counts$both_tp[is.na(timoivar_counts$both_tp)] = 0
timoivar_counts$both_fp[is.na(timoivar_counts$both_fp)] = 0
timoivar_counts$both_fn[is.na(timoivar_counts$both_fn)] = 0
sum(timoivar_counts$both_fp)/(sum(timoivar_counts$both_fp)+sum(timoivar_counts$both_tp))
## [1] 0.0008710801
FPlayer_timoivar = timoivar %>%  filter(Category == "both_fp")
Othertype_timoivar = timoivar %>%  filter(!Category == "both_fp")

Figtimoivar = ggplot() +  
    geom_point(data= Othertype_timoivar, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
    geom_point(data=FPlayer_timoivar, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
  labs(x="timo", y= "ivar") +
  category_colScale_1 +
  theme_bw()+
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 15))+ 
  annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 70.3%", hjust = "left")+
  annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 0.09%", hjust = "left")
## Warning: Ignoring unknown parameters: width
## Warning: Ignoring unknown parameters: width
print(Figtimoivar)
## Warning: Removed 56 rows containing missing values (geom_point).

ggsave(Figtimoivar,
       filename = glue("{workdirectory}/figures_new/Figtimoivar.png"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 56 rows containing missing values (geom_point).
ggsave(Figtimoivar,
       filename = glue("{workdirectory}/figures_pdf/Figtimoivar.pdf"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 56 rows containing missing values (geom_point).
#timo vs freebayes
timofb = merge(Timofreq, freebayesfreq, 
         by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
         by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)

timofb = timofb%>%filter(!Copy_number == "control")
timofb$type.x[is.na(timofb$type.x)] <- "NA"
timofb$type.y[is.na(timofb$type.y)] <- "NA"

timofb = timofb %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp", 
                               ifelse(type.x == type.y & type.x == 'FP', "both_fp", 
                               ifelse(type.x == type.y & type.x == 'FN', "both_fn",
                               ifelse(type.x == "TP" & type.y != "TP", "caller1_tp", 
                               ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp', 
                               ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
                               ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
                                      "NA"))))))))

#calculate both TP%
timofb_bothtp = timofb %>% filter(Category == "both_tp")
#calculate both FP%
timofb_counts = timofb %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
timofb_counts$both_tp[is.na(timofb_counts$both_tp)] = 0
timofb_counts$both_fp[is.na(timofb_counts$both_fp)] = 0
timofb_counts$both_fn[is.na(timofb_counts$both_fn)] = 0
sum(timofb_counts$both_fp)/(sum(timofb_counts$both_fp)+sum(timofb_counts$both_tp))
## [1] 0.001034126
FPlayer_timofb = timofb %>%  filter(Category == "both_fp")
Othertype_timofb = timofb %>%  filter(!Category == "both_fp")

Figtimofb = ggplot() +  
    geom_point(data= Othertype_timofb, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
    geom_point(data=FPlayer_timofb, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
  labs(x="timo", y= "freebayes") +
  geom_point(width = 0.2, alpha = 0.5) +
   category_colScale_1  +
  theme_bw()+
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 15))+ 
  annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 59.2%", hjust = "left")+
  annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 0.10%", hjust = "left")
## Warning: Ignoring unknown parameters: width

## Warning: Ignoring unknown parameters: width

## Warning: Ignoring unknown parameters: width
print(Figtimofb)
## Warning: Removed 97 rows containing missing values (geom_point).

ggsave(Figtimofb,
       filename = glue("{workdirectory}/figures_new/Figtimofb.png"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 97 rows containing missing values (geom_point).
ggsave(Figtimofb,
       filename = glue("{workdirectory}/figures_pdf/Figtimofb.pdf"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 97 rows containing missing values (geom_point).
#timo vs varscan
timovarscan = merge(Timofreq, varscanfreq, 
         by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
         by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)

timovarscan = timovarscan%>%filter(!Copy_number == "control")
timovarscan$type.x[is.na(timovarscan$type.x)] <- "NA"
timovarscan$type.y[is.na(timovarscan$type.y)] <- "NA"

timovarscan = timovarscan %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp", 
                               ifelse(type.x == type.y & type.x == 'FP', "both_fp", 
                               ifelse(type.x == type.y & type.x == 'FN', "both_fn",
                               ifelse(type.x == "TP" & type.y != "TP", "caller1_tp", 
                               ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp', 
                               ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
                               ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
                                      "NA"))))))))

#calculate both TP%
timovarscan_bothtp = timovarscan %>% filter(Category == "both_tp")
#calculate both FP%
timovarscan_counts = timovarscan %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
timovarscan_counts$both_tp[is.na(timovarscan_counts$both_tp)] = 0
timovarscan_counts$both_fp[is.na(timovarscan_counts$both_fp)] = 0
timovarscan_counts$both_fn[is.na(timovarscan_counts$both_fn)] = 0
sum(timovarscan_counts$both_fp)/(sum(timovarscan_counts$both_fp)+sum(timovarscan_counts$both_tp))
## [1] 0.0008733624
FPlayer_timovarscan = timovarscan %>%  filter(Category == "both_fp")
Othertype_timovarscan = timovarscan %>%  filter(!Category == "both_fp")

Figtimovarscan = ggplot() +  
    geom_point(data= Othertype_timovarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
    geom_point(data=FPlayer_timovarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
  labs(x="timo", y= "varscan") +
  geom_point(width = 0.2, alpha = 0.5) +
   category_colScale_1 +
  theme_bw()+
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 15))+ 
  annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 70.1%", hjust = "left")+
  annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 0.09%", hjust = "left")
## Warning: Ignoring unknown parameters: width

## Warning: Ignoring unknown parameters: width

## Warning: Ignoring unknown parameters: width
print(Figtimovarscan)
## Warning: Removed 15 rows containing missing values (geom_point).

ggsave(Figtimovarscan,
       filename = glue("{workdirectory}/figures_new/Figtimovarscan.png"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 15 rows containing missing values (geom_point).
ggsave(Figtimovarscan,
       filename = glue("{workdirectory}/figures_pdf/Figtimovarscan.pdf"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 15 rows containing missing values (geom_point).
#ivar vs hc
ivarhc = merge(ivarfreq, hcfreq, 
         by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
         by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)

ivarhc = ivarhc%>%filter(!Copy_number == "control")
ivarhc$type.x[is.na(ivarhc$type.x)] <- "NA"
ivarhc$type.y[is.na(ivarhc$type.y)] <- "NA"

ivarhc = ivarhc %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp", 
                               ifelse(type.x == type.y & type.x == 'FP', "both_fp", 
                               ifelse(type.x == type.y & type.x == 'FN', "both_fn",
                               ifelse(type.x == "TP" & type.y != "TP", "caller1_tp", 
                               ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp', 
                               ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
                               ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
                                      "NA"))))))))

#calculate both TP%
ivarhc_bothtp = ivarhc %>% filter(Category == "both_tp")
#calculate both FP%
ivarhc_counts = ivarhc %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
ivarhc_counts$both_tp[is.na(ivarhc_counts$both_tp)] = 0
ivarhc_counts$both_fp[is.na(ivarhc_counts$both_fp)] = 0
ivarhc_counts$both_fn[is.na(ivarhc_counts$both_fn)] = 0
sum(ivarhc_counts$both_fp)/(sum(ivarhc_counts$both_fp)+sum(ivarhc_counts$both_tp))
## [1] 0.01701783
Figivarhc = ggplot(ivarhc, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category)) + 
  labs(x="ivar", y= "hc") +
  geom_point(width = 0.2, alpha = 0.5) +
  category_colScale_1 +
  theme_bw()+
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 15))+ 
  annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 74.3%", hjust = "left")+
  annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 1.7%", hjust = "left")
## Warning: Ignoring unknown parameters: width
print(Figivarhc)
## Warning: Removed 1549 rows containing missing values (geom_point).

ggsave(Figivarhc,
       filename = glue("{workdirectory}/figures_new/Figivarhc.png"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 1549 rows containing missing values (geom_point).
ggsave(Figivarhc,
       filename = glue("{workdirectory}/figures_pdf/Figivarhc.pdf"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 1549 rows containing missing values (geom_point).
#ivar vs fb
ivarfb = merge(ivarfreq, freebayesfreq, 
         by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
         by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)

ivarfb = ivarfb%>%filter(!Copy_number == "control")
ivarfb$type.x[is.na(ivarfb$type.x)] <- "NA"
ivarfb$type.y[is.na(ivarfb$type.y)] <- "NA"

ivarfb = ivarfb %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp", 
                               ifelse(type.x == type.y & type.x == 'FP', "both_fp", 
                               ifelse(type.x == type.y & type.x == 'FN', "both_fn",
                               ifelse(type.x == "TP" & type.y != "TP", "caller1_tp", 
                               ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp', 
                               ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
                               ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
                                      "NA"))))))))

#calculate both TP%
ivarfb_bothtp = ivarfb %>% filter(Category == "both_tp")
#calculate both FP%
ivarfb_counts = ivarfb %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
ivarfb_counts$both_tp[is.na(ivarfb_counts$both_tp)] = 0
ivarfb_counts$both_fp[is.na(ivarfb_counts$both_fp)] = 0
ivarfb_counts$both_fn[is.na(ivarfb_counts$both_fn)] = 0
sum(ivarfb_counts$both_fp)/(sum(ivarfb_counts$both_fp)+sum(ivarfb_counts$both_tp))
## [1] 0.04246795
FPlayer_ivarfb = ivarfb %>%  filter(Category == "both_fp")
Othertype_ivarfb = ivarfb %>%  filter(!Category == "both_fp")

Figivarfb = ggplot() +  
    geom_point(data= Othertype_ivarfb, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
    geom_point(data=FPlayer_ivarfb, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
  labs(x="ivar", y= "freebayes") +
  geom_point(width = 0.2, alpha = 0.5) +
  category_colScale_1 +
  theme_bw()+
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 15))+ 
  annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 73.2%", hjust = "left")+
  annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 4.2%", hjust = "left")
## Warning: Ignoring unknown parameters: width

## Warning: Ignoring unknown parameters: width

## Warning: Ignoring unknown parameters: width
print(Figivarfb)
## Warning: Removed 49 rows containing missing values (geom_point).

ggsave(Figivarfb,
       filename = glue("{workdirectory}/figures_new/Figivarfb.png"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 49 rows containing missing values (geom_point).
ggsave(Figivarfb,
       filename = glue("{workdirectory}/figures_pdf/Figivarfb.pdf"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 49 rows containing missing values (geom_point).
#ivar vs varscan
ivarvarscan = merge(ivarfreq, varscanfreq, 
         by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
         by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)

ivarvarscan = ivarvarscan%>%filter(!Copy_number == "control")
ivarvarscan$type.x[is.na(ivarvarscan$type.x)] <- "NA"
ivarvarscan$type.y[is.na(ivarvarscan$type.y)] <- "NA"

ivarvarscan = ivarvarscan %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp", 
                               ifelse(type.x == type.y & type.x == 'FP', "both_fp", 
                               ifelse(type.x == type.y & type.x == 'FN', "both_fn",
                               ifelse(type.x == "TP" & type.y != "TP", "caller1_tp", 
                               ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp', 
                               ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
                               ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
                                      "NA"))))))))

#calculate both TP%
ivarvarscan_bothtp = ivarvarscan %>% filter(Category == "both_tp")
#calculate both FP%
ivarvarscan_counts = ivarvarscan %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
ivarvarscan_counts$both_tp[is.na(ivarvarscan_counts$both_tp)] = 0
ivarvarscan_counts$both_fp[is.na(ivarvarscan_counts$both_fp)] = 0
ivarvarscan_counts$both_fn[is.na(ivarvarscan_counts$both_fn)] = 0
sum(ivarvarscan_counts$both_fp)/(sum(ivarvarscan_counts$both_fp)+sum(ivarvarscan_counts$both_tp))
## [1] 0.01021152
FPlayer_ivarvarscan = ivarvarscan %>%  filter(Category == "both_fp")
Othertype_ivarvarscan = ivarvarscan %>%  filter(!Category == "both_fp")

Figivarvarscan = ggplot() +  
    geom_point(data= Othertype_ivarvarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
    geom_point(data=FPlayer_ivarvarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
  labs(x="ivar", y= "varscan") +
  geom_point(width = 0.2, alpha = 0.5) +
  category_colScale_1 +
  theme_bw()+
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 15))+ 
  annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 83.1%", hjust = "left")+
  annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 1.02%", hjust = "left")
## Warning: Ignoring unknown parameters: width

## Warning: Ignoring unknown parameters: width

## Warning: Ignoring unknown parameters: width
print(Figivarvarscan)
## Warning: Removed 45 rows containing missing values (geom_point).

ggsave(Figivarvarscan,
       filename = glue("{workdirectory}/figures_new/Figivarvarscan.png"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 45 rows containing missing values (geom_point).
ggsave(Figivarvarscan,
       filename = glue("{workdirectory}/figures_pdf/Figivarvarscan.pdf"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 45 rows containing missing values (geom_point).
#hc vs freebayes
hcfb = merge(hcfreq, freebayesfreq, 
         by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
         by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)

hcfb = hcfb%>%filter(!Copy_number == "control")
hcfb$type.x[is.na(hcfb$type.x)] <- "NA"
hcfb$type.y[is.na(hcfb$type.y)] <- "NA"

hcfb = hcfb %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp", 
                               ifelse(type.x == type.y & type.x == 'FP', "both_fp", 
                               ifelse(type.x == type.y & type.x == 'FN', "both_fn",
                               ifelse(type.x == "TP" & type.y != "TP", "caller1_tp", 
                               ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp', 
                               ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
                               ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
                                      "NA"))))))))

#calculate both TP%
hcfb_bothtp = hcfb %>% filter(Category == "both_tp")
#calculate both FP%
hcfb_counts = hcfb %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
hcfb_counts$both_tp[is.na(hcfb_counts$both_tp)] = 0
hcfb_counts$both_fp[is.na(hcfb_counts$both_fp)] = 0
hcfb_counts$both_fn[is.na(hcfb_counts$both_fn)] = 0
sum(hcfb_counts$both_fp)/(sum(hcfb_counts$both_fp)+sum(hcfb_counts$both_tp))
## [1] 0.01821336
Fighcfb = ggplot(hcfb, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category)) + 
  labs(x="hc", y= "freebayes") +
  geom_point(width = 0.2, alpha = 0.5) +
  category_colScale_1 +
  theme_bw()+
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 15))+ 
  annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 69.4%", hjust = "left")+
  annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 1.82%", hjust = "left")
## Warning: Ignoring unknown parameters: width
print(Fighcfb)
## Warning: Removed 1590 rows containing missing values (geom_point).

ggsave(Fighcfb,
       filename = glue("{workdirectory}/figures_new/Fighcfb.png"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 1590 rows containing missing values (geom_point).
ggsave(Fighcfb,
       filename = glue("{workdirectory}/figures_pdf/Fighcfb.pdf"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 1590 rows containing missing values (geom_point).
#hc vs varscan
hcvarscan = merge(hcfreq, varscanfreq, 
         by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
         by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)

hcvarscan = hcvarscan%>%filter(!Copy_number == "control")
hcvarscan$type.x[is.na(hcvarscan$type.x)] <- "NA"
hcvarscan$type.y[is.na(hcvarscan$type.y)] <- "NA"

hcvarscan = hcvarscan %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp", 
                               ifelse(type.x == type.y & type.x == 'FP', "both_fp", 
                               ifelse(type.x == type.y & type.x == 'FN', "both_fn",
                               ifelse(type.x == "TP" & type.y != "TP", "caller1_tp", 
                               ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp', 
                               ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
                               ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
                                      "NA"))))))))

#calculate both TP%
hcvarscan_bothtp = hcvarscan %>% filter(Category == "both_tp")
#calculate both FP%
hcvarscan_counts = hcvarscan %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
hcvarscan_counts$both_tp[is.na(hcvarscan_counts$both_tp)] = 0
hcvarscan_counts$both_fp[is.na(hcvarscan_counts$both_fp)] = 0
hcvarscan_counts$both_fn[is.na(hcvarscan_counts$both_fn)] = 0
sum(hcvarscan_counts$both_fp)/(sum(hcvarscan_counts$both_fp)+sum(hcvarscan_counts$both_tp))
## [1] 0.0084246
Fighcvarscan = ggplot(hcvarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category)) + 
  labs(x="hc", y= "varscan") +
  geom_point(width = 0.2, alpha = 0.5) +
  category_colScale_1 +
  theme_bw()+
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 15))+ 
  annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 72.1%", hjust = "left")+
  annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 0.84%", hjust = "left")
## Warning: Ignoring unknown parameters: width
print(Fighcvarscan)
## Warning: Removed 1530 rows containing missing values (geom_point).

ggsave(Fighcvarscan,
       filename = glue("{workdirectory}/figures_new/Fighcvarscan.png"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 1530 rows containing missing values (geom_point).
ggsave(Fighcvarscan,
       filename = glue("{workdirectory}/figures_pdf/Fighcvarscan.pdf"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 1530 rows containing missing values (geom_point).
#fb vs varscan
fbvarscan = merge(freebayesfreq, varscanfreq, 
         by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
         by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)

fbvarscan = fbvarscan%>%filter(!Copy_number == "control")
fbvarscan$type.x[is.na(fbvarscan$type.x)] <- "NA"
fbvarscan$type.y[is.na(fbvarscan$type.y)] <- "NA"

fbvarscan = fbvarscan %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp", 
                               ifelse(type.x == type.y & type.x == 'FP', "both_fp", 
                               ifelse(type.x == type.y & type.x == 'FN', "both_fn",
                               ifelse(type.x == "TP" & type.y != "TP", "caller1_tp", 
                               ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp', 
                               ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
                               ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
                                      "NA"))))))))

#calculate both TP%
fbvarscan_bothtp = fbvarscan %>% filter(Category == "both_tp")
#calculate both FP%
fbvarscan_counts = fbvarscan %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
fbvarscan_counts$both_tp[is.na(fbvarscan_counts$both_tp)] = 0
fbvarscan_counts$both_fp[is.na(fbvarscan_counts$both_fp)] = 0
fbvarscan_counts$both_fn[is.na(fbvarscan_counts$both_fn)] = 0
sum(fbvarscan_counts$both_fp)/(sum(fbvarscan_counts$both_fp)+sum(fbvarscan_counts$both_tp))
## [1] 0.01125541
FPlayer_fbvarscan = fbvarscan %>%  filter(Category == "both_fp")
Othertype_fbvarscan = fbvarscan %>%  filter(!Category == "both_fp")

Figfbvarscan = ggplot() +  
    geom_point(data= Othertype_fbvarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
    geom_point(data=FPlayer_fbvarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
  labs(x="freebayes", y= "varscan") +
  geom_point(width = 0.2, alpha = 0.5) +
  category_colScale_1 +
  theme_bw()+
  theme(axis.title = element_text(size = 15))+
  theme(legend.text = element_text(size = 15))+ 
  annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 70.0%", hjust = "left")+
  annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 1.13%", hjust = "left")
## Warning: Ignoring unknown parameters: width

## Warning: Ignoring unknown parameters: width

## Warning: Ignoring unknown parameters: width
print(Figfbvarscan)
## Warning: Removed 88 rows containing missing values (geom_point).

ggsave(Figfbvarscan,
       filename = glue("{workdirectory}/figures_new/Figfbvarscan.png"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 88 rows containing missing values (geom_point).
ggsave(Figfbvarscan,
       filename = glue("{workdirectory}/figures_pdf/Figfbvarscan.pdf"),
       width = 5,
       height = 4, limitsize=FALSE)#, useDingbats = FALSE)
## Warning: Removed 88 rows containing missing values (geom_point).

How does having cutoffs affect variant calling? - Fig S7B,S7C, Fig 4C & 4D

#Construct cutoff df

#Loop through a vector of frequency cutoffs and read depth cutoffs

freq_list = c(0, 0.01, 0.02, 0.03)
rd_list = c(0, 100, 200, 300)

vdf_filt = data.frame()

for(f in freq_list){
    #print(f)
    
    for(c in rd_list){
    
        #print(c)
        
        #print(dim(filt_vdf))
        
        fv = vcf_plus %>%
                mutate(new_category = ifelse(ALT_FREQ >= f & gt_DP >= c & type == 'TP',
                                            "TP",
                                            ifelse(ALT_FREQ < f & type == 'TP'| 
                                                   gt_DP < c & type == 'TP',
                                                  "FN", 
                                                  ifelse(type == 'FN',
                                                        "FN", 
                                                        ifelse(type == 'FP' & ALT_FREQ >= f & gt_DP >= c,
                                                              "FP", "TN")))))
        
        fv$freq_cut = f
        
        fv$cov_cut = c
        
        vdf_filt = rbind(vdf_filt, fv)       
    }
}

dim(vdf_filt)
## [1] 520672     47
#colnames(vdf_filt)

vdf_filt$category = vdf_filt$new_category

#calculate the number of TP, FP, FN after filtering
message("Category count for filt data")
## Category count for filt data
vdf_filt = vdf_filt %>% ungroup() %>% unique()

group_columns = c('category',"vcf_inputs",'freq_cut','cov_cut', "Expected_freq", "Copy_number", "Rep")

count_filt = vdf_filt %>% 
            group_by(across(all_of(group_columns))) %>%
            add_tally(name = 'category_count') %>%
            ungroup() %>% 
            select(all_of(c(group_columns, 'category_count'))) %>%
            unique() 

# Load function: adjust_count
adjust_counts = function(count_df){

    count_df = count_df %>%
                pivot_wider(names_from = category, values_from = category_count)

    if (!"FP" %in% colnames(count_df)){

      print("No false-positives - adjusting")

      count_df$FP = 0

    }else{print("FP present - no adjustment needed")}

    count_df[is.na(count_df)] = 0

    count_df$TPR = count_df$TP/(count_df$TP + count_df$FN)

    count_df$PPV = count_df$TP/(count_df$TP + count_df$FP)

    count_df$FNR = count_df$FN/(count_df$FN + count_df$TP)

    count_df$FDR = count_df$FP/(count_df$FP + count_df$TP)

    count_df$F1 = 2 * ((count_df$PPV * count_df$TPR)/(count_df$PPV + count_df$TPR))

    count_df[is.na(count_df)] = 0

    #count_df$gt_DP = as.numeric(as.character(count_df$gt_DP))

    return(count_df)
}

# put that count dataframe into the 'adjust_counts' function
message("Adjust filtered count df")
## Adjust filtered count df
df_filt = adjust_counts(count_filt)
## [1] "FP present - no adjustment needed"
df_filt = df_filt %>% filter (cov_cut == "0", Rep == "rep1") %>% group_by(cov_cut, freq_cut, vcf_inputs, Expected_freq, Copy_number, Rep) %>% mutate(TP_percentage = TP/(TP + FN + FP), FP_percentage = FP/(TP + FN + FP), FN_percentage = FN/(TP + FN + FP)) %>% unique() %>% group_by(Copy_number, vcf_inputs, freq_cut, cov_cut) %>% mutate(Mean_TP = mean(TP_percentage), sd_TP = sd(TP_percentage))%>% group_by(Copy_number, vcf_inputs, freq_cut, cov_cut) %>% mutate(Mean_FP = mean(FP_percentage), sd_FP = sd(FP_percentage))%>% group_by(Copy_number, vcf_inputs, freq_cut, cov_cut) %>% mutate(Mean_FN = mean(FN_percentage), sd_FN = sd(FN_percentage))
df_filt = df_filt %>% filter(Copy_number != "control")

df_filt$freq_cut = as.character(df_filt$freq_cut)



#update replicates df with new SNV_info   

rep1 = vcf_plus %>% filter(Rep == "rep1") %>% filter(!FerretID %in% c("Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix44"))
rep2 = vcf_plus %>% filter(Rep == "rep2") %>% filter(!FerretID %in% c("Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix44"))

# merge the replicates 
replicates = merge(rep1, rep2, 
by.x =c('CHROM', "Copy_number", "POS", "Expected_freq", "REF", "ALT", "ChromKey", "vcf_inputs", "Use", "Cohort", "repname"),

by.y = c('CHROM', "Copy_number", "POS", "Expected_freq", "REF", "ALT", "ChromKey", "vcf_inputs", "Use", "Cohort", "Sample"),  all = T)
#Change NA to zero 
replicates$ALT_FREQ.x[is.na(replicates$ALT_FREQ.x)] = 0
replicates$ALT_FREQ.y[is.na(replicates$ALT_FREQ.y)] = 0
replicates$type.x[is.na(replicates$type.x)] = "NONE"
replicates$type.y[is.na(replicates$type.y)] = "NONE"
# Remove the controls for this analysis 
replicates = replicates %>% filter(!Copy_number == "control")

# specify the four categories 

replicates = replicates %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp", 
                               ifelse(type.x == type.y & type.x == 'FP', "both_fp", 
                               ifelse(type.x == "TP" & type.y != "TP", "rep1_tp", 
                               ifelse(type.x != "TP" & type.y == 'TP', 'rep2_tp', 
                               ifelse(type.x == 'FN' & type.x == type.y, "both_fn",
                               ifelse(type.x == 'FP' & type.y != 'FP' | type.x != 'FP' & type.y == 'FP', 'single_fp', "NA")))))))  
  
across_replicates = replicates %>% filter(Category == "both_tp" | Category =="both_fp" |Category =="both_fn")

#Count the number of TP, FN, FP
type_counts_two_rep = across_replicates %>% group_by(Expected_freq, Category, vcf_inputs, Copy_number, CHROM) %>% add_tally(name = 'type_count') %>% ungroup() %>% select(Expected_freq, Category,type_count, vcf_inputs, Copy_number, CHROM) %>% unique()

#make sure for each expected freq + copy number set, the sum of TP & FN is the same (becuase combined they are the total number of SNVs)
type_counts_two_rep =  type_counts_two_rep %>% pivot_wider(names_from = Category, values_from = type_count) 
#type_counts_individual_rep[is.na(type_counts_individual_rep)] = 0
type_counts_two_rep$both_fp[is.na(type_counts_two_rep$both_fp)] = 0
type_counts_two_rep$both_tp[is.na(type_counts_two_rep$both_tp)] = 0


type_counts_two_rep = across_replicates %>% group_by(Expected_freq, Category, vcf_inputs, Copy_number) %>% add_tally(name = 'type_count') %>% ungroup() %>% select(Expected_freq, Category,type_count, vcf_inputs, Copy_number) %>% unique()

#make sure for each expected freq + copy number set, the sum of TP & FN is the same (becuase combined they are the total number of SNVs)
type_counts_two_rep =  type_counts_two_rep %>% pivot_wider(names_from = Category, values_from = type_count) 
#type_counts_individual_rep[is.na(type_counts_individual_rep)] = 0
type_counts_two_rep$both_fp[is.na(type_counts_two_rep$both_fp)] = 0
type_counts_two_rep$both_tp[is.na(type_counts_two_rep$both_tp)] = 0
#type_counts_individual_rep = type_counts_individual_rep %>% group_by(Expected_freq,vcf_inputs) %>% mutate(SNV_count = both_fn + both_tp)
type_counts_two_rep["Rep"] = "Merged"
colnames(type_counts_two_rep)[4] <- "FN"
colnames(type_counts_two_rep)[5] <- "TP"
colnames(type_counts_two_rep)[6] <- "FP"

#Calculate TP percentage and FP percentage
type_counts_two_rep = type_counts_two_rep %>% group_by(vcf_inputs, Expected_freq, Copy_number) %>% mutate(TP_percentage = TP/(TP + FN + FP), FP_percentage = FP/(TP + FP), FN_percentage = FN/(TP + FN)) %>% unique() #%>% group_by(Copy_number, vcf_inputs) %>% mutate(Mean_TP = mean(TP_percentage), sd_TP = sd(TP_percentage))%>% group_by(Copy_number, vcf_inputs) %>% mutate(Mean_FP = mean(FP_percentage), sd_FP = sd(FP_percentage))%>% group_by(Copy_number, vcf_inputs) %>% mutate(Mean_FN = mean(FN_percentage), sd_FN = sd(FN_percentage))

type_counts_two_rep$FP_percentage[is.na(type_counts_two_rep$FP_percentage)] = 0
type_counts_two_rep$FN_percentage[is.na(type_counts_two_rep$FN_percentage)] = 0



FigS7B = ggplot()+
geom_line(data = df_filt %>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")), 
            aes(x=Expected_freq, 
                y = FDR,  
                group = interaction(freq_cut, Copy_number), 
                linetype = freq_cut,
                color = vcf_inputs), alpha = 0.8, size = 1) +
  geom_point(data=df_filt%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")),
                aes(x=Expected_freq, y=FDR, 
                    colour = vcf_inputs, shape = Copy_number), 
             alpha = 0.9, size = 2) +

  geom_line(data = type_counts_two_rep%>% filter( Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")), 
            aes(x=Expected_freq, y= FP_percentage, 
                group = interaction(Rep, Copy_number)),
           color = 'black', 
           alpha = 0.8)+
  geom_point(data=type_counts_two_rep%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")),
                aes(x=Expected_freq, y= FP_percentage, shape = Copy_number,),
             color = 'black',
             alpha = 0.9)+
  tool_colScale + 
  
  #labs(x="Copy Number", y= "FDR") +
  
  theme_bw() +
  
  facet_grid(Copy_number~vcf_inputs) +
  
  theme(legend.key = element_blank(),
                strip.background = element_rect(colour="black", fill="white"),
              axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS7B)

ggsave(FigS7B,
       filename = glue("{workdirectory}/figures_pdf_new/FigS7B.pdf"),  
       width = 9,
       height = 5, limitsize=FALSE, useDingbats = FALSE)

FigS7B_2 = ggplot()+
geom_line(data = df_filt %>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")), 
            aes(x=Expected_freq, 
                y = FDR,  
                group = interaction(freq_cut, Copy_number), 
                linetype = freq_cut,
                color = vcf_inputs), alpha = 0.8, size = 1) +
  geom_point(data=df_filt%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")),
                aes(x=Expected_freq, y=FDR, 
                    colour = vcf_inputs, shape = Copy_number), 
             alpha = 0.9, size = 2) +

  geom_line(data = type_counts_two_rep%>% filter( Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")), 
            aes(x=Expected_freq, y= FP_percentage, 
                group = interaction(Rep, Copy_number)),
           color = 'black', 
           alpha = 0.8)+
  geom_point(data=type_counts_two_rep%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")),
                aes(x=Expected_freq, y= FP_percentage, shape = Copy_number,),
             color = 'black',
             alpha = 0.9)+
  tool_colScale + 
  
  #labs(x="Copy Number", y= "FDR") +
  
  theme_bw() +
  
  facet_grid(Copy_number~vcf_inputs) +
  
  theme(legend.key = element_blank(),
                strip.background = element_rect(colour="black", fill="white"),
              axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS7B_2)

ggsave(FigS7B_2,
       filename = glue("{workdirectory}/figures_pdf_new/FigS7B_2.pdf"),  
       width = 7,
       height = 5, limitsize=FALSE, useDingbats = FALSE)


FigS7C = ggplot()+
geom_line(data = df_filt %>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")), 
            aes(x=Expected_freq, 
                y = FNR,  
                group = interaction(freq_cut, Copy_number), 
                linetype = freq_cut,
                color = vcf_inputs), alpha = 0.8, size = 1) +
  geom_point(data=df_filt%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")),
                aes(x=Expected_freq, y=FNR, 
                    colour = vcf_inputs, shape = Copy_number), 
             alpha = 0.9, size = 2) +

  geom_line(data = type_counts_two_rep%>% filter( Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")), 
            aes(x=Expected_freq, y= FN_percentage, 
                group = interaction(Rep, Copy_number)),
           color = 'black', 
           alpha = 0.8)+
  geom_point(data=type_counts_two_rep%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")),
                aes(x=Expected_freq, y= FN_percentage, shape = Copy_number,),
             color = 'black',
             alpha = 0.9)+
  tool_colScale + 
  
  #labs(x="Copy Number", y= "FDR") +
  
  theme_bw() +
  
  facet_grid(Copy_number~vcf_inputs) +
  
  theme(legend.key = element_blank(),
                strip.background = element_rect(colour="black", fill="white"),
              axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS7C)

ggsave(FigS7C,
       filename = glue("{workdirectory}/figures_pdf_new/FigS7C.pdf"),  
       width = 9,
       height = 5, limitsize=FALSE, useDingbats = FALSE)

FigS7C_2 = ggplot()+
geom_line(data = df_filt %>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")), 
            aes(x=Expected_freq, 
                y = FNR,  
                group = interaction(freq_cut, Copy_number), 
                linetype = freq_cut,
                color = vcf_inputs), alpha = 0.8, size = 1) +
  geom_point(data=df_filt%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")),
                aes(x=Expected_freq, y=FNR, 
                    colour = vcf_inputs, shape = Copy_number), 
             alpha = 0.9, size = 2) +

  geom_line(data = type_counts_two_rep%>% filter( Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")), 
            aes(x=Expected_freq, y= FN_percentage, 
                group = interaction(Rep, Copy_number)),
           color = 'black', 
           alpha = 0.8)+
  geom_point(data=type_counts_two_rep%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")),
                aes(x=Expected_freq, y= FN_percentage, shape = Copy_number,),
             color = 'black',
             alpha = 0.9)+
  tool_colScale + 
  
  #labs(x="Copy Number", y= "FDR") +
  
  theme_bw() +
  
  facet_grid(Copy_number~vcf_inputs) +
  
  theme(legend.key = element_blank(),
                strip.background = element_rect(colour="black", fill="white"),
              axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS7C_2)

ggsave(FigS7C_2,
       filename = glue("{workdirectory}/figures_pdf_new/FigS7C_2.pdf"),  
       width = 7,
       height = 5, limitsize=FALSE, useDingbats = FALSE)

# Looking at 10^5 only

Fig4C = ggplot()+
geom_line(data = df_filt %>% filter( Copy_number == "10^5"), 
            aes(x=Expected_freq, 
                y = FDR, 
                group = freq_cut, 
                linetype = freq_cut,
                color = vcf_inputs), alpha = 0.8, size = 1) +
  geom_point(data=df_filt%>% filter( Copy_number == "10^5"),
                aes(x=Expected_freq, y=FDR, 
                    colour = vcf_inputs), 
             alpha = 0.9, size = 2) +

  geom_line(data = type_counts_two_rep%>% filter( Copy_number == "10^5"), 
            aes(x=Expected_freq, y= FP_percentage, 
                group = Rep),
           color = 'black', 
           alpha = 0.8)+
  geom_point(data=type_counts_two_rep%>% filter( Copy_number == "10^5"),
                aes(x=Expected_freq, y= FP_percentage),
             color = 'black',
             alpha = 0.9)+
  tool_colScale + 
  
  #labs(x="Copy Number", y= "FDR") +
  
  theme_bw() +
  
  facet_grid(.~vcf_inputs) +
  
  theme(legend.key = element_blank(),
                strip.background = element_rect(colour="black", fill="white"),
              axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(Fig4C)

ggsave(Fig4C,
       filename = glue("{workdirectory}/figures_pdf_new/Fig4C.pdf"),  
       width = 15,
       height = 4, limitsize=FALSE, useDingbats = FALSE)

Fig4D = ggplot()+
geom_line(data = df_filt %>% filter( Copy_number == "10^5"), 
            aes(x=Expected_freq, 
                y = FNR, 
                group = freq_cut, 
                linetype = freq_cut,
                color = vcf_inputs), alpha = 0.8, size = 1) +
  geom_point(data=df_filt%>% filter( Copy_number == "10^5"),
                aes(x=Expected_freq, y=FNR, 
                    colour = vcf_inputs), 
             alpha = 0.9, size = 2) +

  geom_line(data = type_counts_two_rep%>% filter( Copy_number == "10^5"), 
            aes(x=Expected_freq, y= FN_percentage, 
                group = Rep),
           color = 'black', 
           alpha = 0.8)+
  geom_point(data=type_counts_two_rep%>% filter( Copy_number == "10^5"),
                aes(x=Expected_freq, y= FN_percentage),
             color = 'black',
             alpha = 0.9)+
  tool_colScale + 
  
  #labs(x="Copy Number", y= "FDR") +
  
  theme_bw() +
  
  facet_grid(.~vcf_inputs) +
  
  theme(legend.key = element_blank(),
                strip.background = element_rect(colour="black", fill="white"),
              axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(Fig4D)

ggsave(Fig4D,
       filename = glue("{workdirectory}/figures_pdf_new/Fig4D.pdf"),  
       width = 15,
       height = 4, limitsize=FALSE, useDingbats = FALSE)

FigS8C & S8D

df_filt = adjust_counts(count_filt)
## [1] "FP present - no adjustment needed"
df_filt = df_filt %>% filter(freq_cut == "0", Rep == "rep1") %>% group_by(cov_cut, freq_cut, vcf_inputs, Expected_freq, Copy_number, Rep) %>% mutate(TP_percentage = TP/(TP + FN + FP), FP_percentage = FP/(TP + FN + FP), FN_percentage = FN/(TP + FN + FP)) %>% unique() %>% group_by(Copy_number, vcf_inputs, freq_cut, cov_cut) %>% mutate(Mean_TP = mean(TP_percentage), sd_TP = sd(TP_percentage))%>% group_by(Copy_number, vcf_inputs, freq_cut, cov_cut) %>% mutate(Mean_FP = mean(FP_percentage), sd_FP = sd(FP_percentage))%>% group_by(Copy_number, vcf_inputs, freq_cut, cov_cut) %>% mutate(Mean_FN = mean(FN_percentage), sd_FN = sd(FN_percentage))
df_filt = df_filt %>% filter(Copy_number != "control")
df_filt$cov_cut = as.character(df_filt$cov_cut)

FigS8C = ggplot()+
geom_line(data = df_filt %>% filter( Copy_number == "10^5"), 
            aes(x=Expected_freq, 
                y = FDR, 
                group = cov_cut, 
                linetype = cov_cut,
                color = vcf_inputs), alpha = 0.8, size = 1) +
  geom_point(data=df_filt%>% filter( Copy_number == "10^5"),
                aes(x=Expected_freq, y=FDR, 
                    colour = vcf_inputs), 
             alpha = 0.9, size = 2) +

  geom_line(data = type_counts_two_rep%>% filter( Copy_number == "10^5"), 
            aes(x=Expected_freq, y= FP_percentage, 
                group = Rep),
           color = 'black', 
           alpha = 0.8)+
  geom_point(data=type_counts_two_rep%>% filter( Copy_number == "10^5"),
                aes(x=Expected_freq, y= FP_percentage),
             color = 'black',
             alpha = 0.9)+
  tool_colScale + 
  
  #labs(x="Copy Number", y= "FDR") +
  
  theme_bw() +
  facet_grid(.~vcf_inputs) +
  
  theme(legend.key = element_blank(),
                strip.background = element_rect(colour="black", fill="white"),
              axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS8C)

ggsave(FigS8C,
       filename = glue("{workdirectory}/figures_pdf_new/FigS8C.pdf"),  
       width = 15,
       height = 4, limitsize=FALSE, useDingbats = FALSE)

FigS8D = ggplot()+
geom_line(data = df_filt %>% filter( Copy_number == "10^5"), 
            aes(x=Expected_freq, 
                y = FNR, 
                group = cov_cut, 
                linetype = cov_cut,
                color = vcf_inputs), alpha = 0.8, size = 1) +
  geom_point(data=df_filt%>% filter( Copy_number == "10^5"),
                aes(x=Expected_freq, y=FNR, 
                    colour = vcf_inputs), 
             alpha = 0.9, size = 2) +

  geom_line(data = type_counts_two_rep%>% filter( Copy_number == "10^5"), 
            aes(x=Expected_freq, y= FN_percentage, 
                group = Rep),
           color = 'black', 
           alpha = 0.8)+
  geom_point(data=type_counts_two_rep%>% filter( Copy_number == "10^5"),
                aes(x=Expected_freq, y= FN_percentage),
             color = 'black',
             alpha = 0.9)+
  tool_colScale + 
  
  #labs(x="Copy Number", y= "FDR") +
  
  theme_bw() +
  facet_grid(.~vcf_inputs) +
  
  theme(legend.key = element_blank(),
                strip.background = element_rect(colour="black", fill="white"),
              axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS8D)

ggsave(FigS8D,
       filename = glue("{workdirectory}/figures_pdf_new/FigS8D.pdf"),  
       width = 15,
       height = 4, limitsize=FALSE, useDingbats = FALSE)

Fig3B

FP = vcf_plus %>% filter(type == "FP", Copy_number != "control")
FP%>% filter(ALT_FREQ>0.75)
##  [1] POS                    CHROM                  REF                   
##  [4] ALT                    Copy_number            Expected_freq         
##  [7] vcf_inputs             Rep                    filename              
## [10] ChromKey               ID                     REF_COUNT             
## [13] ALT_COUNT              gt_DP                  sample                
## [16] REF_FREQ               ALT_FREQ               ALT_TYPE              
## [19] majorfreq              minorfreq              major                 
## [22] minor                  CHROM_SIZE             GENOME_SIZE           
## [25] LibraryPosition        SampleInfo             Use                   
## [28] Cohort                 FerretID               Sample                
## [31] repname                MRTPCR_Date            MTRPCR_Plate          
## [34] PostCleanUpConc        PostAmpConc            PostDilutionConc      
## [37] i5                     i5_Tuboweb             i7                    
## [40] i7_TuboWeb             Adaptor.IDs            TrueExpectedCopyNumber
## [43] TrueExpectedFrequency  type                  
## <0 rows> (or 0-length row.names)
PlotTheme1 = theme_bw() +
            theme(legend.key = element_blank(),
                  strip.background = element_rect(colour= "black", fill= "white"),
                  axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))

plot3b1 = ggplot(FP, aes(x=ALT_FREQ, y = gt_DP, color = vcf_inputs)) + 
    geom_point(alpha = 0.8, size = 2) + 
    tool_colScale +
    PlotTheme1 +
    geom_hline(yintercept = 500, linetype = 2, color = 'black') + 
    geom_vline(xintercept = 0.03, linetype = 2, color = 'black') + 
    theme(legend.position = 'NONE') + 
    labs(x="allele frequency", y = 'read depth')
print(plot3b1)

ggsave(plot3b1,
       filename = glue("{workdirectory}/figures_pdf_new/Fig3B1_flu_synthetic.pdf"),
       width = 4,
       height = 4, limitsize=FALSE, useDingbats = FALSE)

plot3b2 = ggplot(FP, aes(x=gt_DP, fill = vcf_inputs)) + 
    geom_histogram(binwidth = 500) + 
    tool_colScale_fill +
    PlotTheme1 +
    theme(legend.position = 'NONE') + 
    labs(x="read depth", y= "false positive count") +
   # facet_grid(.~vcf_inputs) +
    coord_flip() +
    scale_x_continuous(position = "top")
print(plot3b2)

ggsave(plot3b2,
       filename = glue("{workdirectory}/figures_pdf_new/Fig3B2_flu_synthetic.pdf"),
       width = 2,
       height = 4, limitsize=FALSE, useDingbats = FALSE)

plot3b3 = ggplot(FP, aes(x=ALT_FREQ, fill = vcf_inputs)) + 
    geom_histogram(binwidth = 0.02) + 
    tool_colScale_fill +
    PlotTheme1 +
    theme(legend.position = 'NONE') + 
    labs(x="allele frequency", y = 'false positive count')+
    scale_x_continuous(position = "top")
print(plot3b3)

ggsave(plot3b3,
       filename = glue("{workdirectory}/figures_pdf_new/Fig3B3_flu_synthetic.pdf"),
       width = 4,
       height = 2, limitsize=FALSE, useDingbats = FALSE)